Story Ideas;

Naruto/Fairy Tail Crossover: I had the idea of what if Naruto Uzumaki was Natsu Dragneel. He was born to Kushina Uzumaki and Minato Namikaze and has pink hair because its a balance between his parents hair. The night he is born the Kyuubi is still released but his twin sister is the Jinchuuriki instead and both parents survive. Danzo and the council convince Sarutobi to tell Minato and Kushina that Naruto died. In their grief and fear that the Masked Man may come after their Jinchuuriki daughter, they tell Sarutobi to inform the village they all died and the Kyuubi is gone. They would take their daughter away in secret to raise her and train her to one day combat the masked man. Sarutobi agrees, but knows without a Jinchuuriki that the village would be vulnerable. Taking another suggestion from Danzo, they announce to the village that Minato and Kushina died, but the still alive Naruto holds the Kyuubi. This is done so that information will leak that there is still a Jinchuuriki in Konoha, but hearing the bloodlust from the Village, Sarutobi regrets his decision. So he passes the law that no one of the next generation is to learn of Naruto's status. This would hopefully mean that Naruto can still have a normal childhood, or at least survive until Minato and Kushina return, but he is wrong. He still grows up ostracized and hated. When he is about three or four, after losing a fight to Sasuke, he is attacked and taken out of the Village to be killed. That is when the Fire Dragon Igneel, flying over the forests of fire country discovers him. The people, terrified of the fierce some dragon attack and are killed, but Naruto survives the traumatic experience. When he awakes, he has no recollection of his previous life, and Igneel, seeing what his own people were going to do to him, decides to adopt him. When Igneel asks Naruto his name, all he can recall is the Na- part. Igneel, being creative (sarcasm), decided to combine Na with Tatsu which means dragon and comes up with the name Natsu. Igneel takes the newly dubbed Natsu to Fiore. From there we follow Fairy Tail canon story.

Back in Konoha, Minato and Kushina return with a 10 year old daughter, ready to take up the mantle again. From their, all of Sarutobi's lies unravel and the Namikaze family is left grief stricken. Years later, their daughter, while on mission to escort cargo to a far away port in a place called Fiore, winds up in a port town called Hargeon. There she encounters a boy called Salamander and she instinctively know they are connected (that whole twin connection thing). She sends a message back to Konoha saying she may have found her brother and waits for response. Minato and Kushina, wanting to believe, put togther a team of Jiraiya and other information gathering specialist and uses the Hokage Guard Platoon to Hiraishin to his daughter in Fiore. It is risky because the Hiraishin has never been used to that great a distance. They make it and they investigate and eventually find Natsu at Fairy Tail. After a while they manage to get a DNA sample to test and Jiraiya returns to Konoha via reverse summon. Once confirmed the Namikazes go to Fiore and confront Natsu, who doesn't believe any of what they are talking about. He is in denial for a long time, probably up to the Tenrou Island incident.

I can think of a couple of things to add to this story to make overlap fun:

Natsu has residual memory of his fight and loss with Sasuke, and that is why he doesn't get along with Grey.

Tenten going Fangirl on Erza.

Gajeel always asking Tenten for a snack.

A Female Haku, Grey, Juvia love triangle (At least is Juvia's mind, Haku and Grey just get along very well).

Jiraiya would have a field day with all the women in Fiore.

Maybe Tsunade having a mother/daughter relationship with Wendy.

Sakura and Porlyusica meeting (Comedy waiting to happen).

Lucy and Ino being considered clones.

Anko and Cana (Thick ass thieves those two would be).

Hinata and Mirajane would get along well (Maybe Mirajane helps Hinata out of her shell).

I can also see, way down the line of the story, the Elemental Nations, and Akatsuki having teams at the Grand Magic Games.

I would also like to see more than a couple of fights between characters of each series:

Sasuke vs Natsu (Natsu eats all of Sasuke's fire attacks, and Natsu is great at hand to hand)

Raikage A vs Laxus (Similar styles of fighting, only Laxus can absorb A's power)

Zabuza vs Gajeel (Gajeel eats Zabuza Sword, Zabuza repairs it)

Naruto/Modern Warfare: Naruto doesn't become a ninja and goes into seclusion in a private area of the village. He develops modern firearms and weapons technology, but he only fights for what he wants to fight for. Idea for beginning: 1. While Orochimaru and Sandaime are fighting on the roof of the chuunin exams, Naruto uses a .50 cal. to blow off both of orochimaru's arms, but no one knows what happens at first. 2. Hinata's entire team gets captured by Kumo and Naruto launches a rescue (he does this because she was kind to him once before) to get them back.
Elements of Call of Duty: Modern Warfare 1-3, SOCOM Navy SEALs, Medal of Honor and any other modern warfare source.
Whether Naruto still has Kyuubi or not is irrelevant. If Minato and Kushina are still alive, they must raise a twin, and any other children they have, away from the village in secret and return after 12 years. Naruto can't know how to use chakra (he never learned and never learns later on).

Naruto/Modern Warfare 2: Naruto disappears at 6 years old and doesn't reappear for 10-12 years. When he reappears he is tight lipped about where he was and has no interest in helping the village. He lives in the Village for the next two years running a repair shop. Then, when Hinata's team is on a mission they all get captured by Kumo. When Naruto hears what has happened he has a flashback to before he disappeared from the village about Hinata and how he feels he owes her for the one time anyone showed him kindness in the village, and decides to rescue Hinata and her team. He doesn't do it alone because that would be suicide so he does something he swore he would never do again. He digs out a satellite phone that he hid from everyone, including the ANBU who used to search his place when he first got back to make sure he wasn't a spy or traitor. He dials a number and contacts some old friends for help. He then goes and collects some gear and slips out of the village to meet his friends.
For this one I am thinking that Naruto disappeared and wound up being spotted first in the World of Call of Duty Modern Warfare 1, the first mission on the ship. While price and everyone is leaving the ship they spot someone in the water and save him, it turns out to be Naruto. Through some turn of events he proves himself capable of learning combat (he did some conditioning training to prepare him for the Ninja academy that he never got to attend). He learns a little from Captain Price before his team gets wiped out at the end of "Modern Warfare" one and learns the rest from Soap. He leaves the group to travel the world and meets the guys from the Expendables movies. He hooks up with them for a while before deciding to find a way back home. It takes him 6 monthes to find the elemental nations again and when he leaves the Expendables they tell him that he will always be a part of them and said to call he ever needed anything. So that is who he calls to help rescue Hinata's team.
The do's and Dont's of this story: 1. Naruto cannot know any or learn any jutsu later. Naruto will be capable of using any modern type weaponry, even the ones seen in movies and games, except jets (he can fly helicopters and small single engine or dual engine airplanes). However, all weapons must be true modern and not sci-fi.

Naruto/Sci-fi: Naruto develops weapon technology from our future point of view. Technology that must be used, is the nano technology from Red Faction and Red Faction redemption (along with weapons and battle suits), the dimension compression technology from Ultraviolet (ninja's have scrolls, Naruto will have these). The weapons from RAGE the video-game (particularly the self aiming shuriken, the spider bots, and the sentry turrets). The jet pack and other helghaust weapons from killzone 1-3. But naruto must develop the weapons on his own. No found lost technology of a forgotten or lost age. He will be a science and technology genius.
Whether naruto still has Kyuubi or not is irrelevant. If Minato and Kushina are still alive, they must raise a twin, and any other children they have, away from the village in secret and return after 12 years. Naruto can't use chakra in this story (he never learned and never learns later on).

Naruto/Bio-weapons: Naruto has a friend murdered in front of him at a young age. After this happens and all those involved are set free without punishment by the council he disappears, everyone thinking he escaped the village. But he really finds one of Orochimaru's old hideouts, and after exploring a section of the floor gives way and he finds an old super computer farm that Orochimaru didn't know about. There he learns about viral weaponry (Elements of Resident Evil and Prototype will be used), and plots revenge on not only Konoha, but all of mankind. Elements here that are used are the T-Virus, G-Virus, T-veronica Virus, Las Plagus, Blacklight Virus.
Things that must happen are that Naruto starts with the same abilities as Albert Wesker. He must sell the G-virus to the Fourth Mizukage to use against bloodline bearers. The t-virus must be unleashed during the sand/sound invasion.
Naruto must have an alliance with Orochimaru, this happens by them meeting in the forest of death during the chuunin exams and Naruto offers Orochimaru the true secret to immortality. He does this by offering a demonstration of his knowledge and sources (this is done by the t-virus release during the invasion). Naruto uses Orochimaru to get him out of Konoha and search for Elizabeth Greene. During the search he finds the Las Plagus and secret develops them to build his own private force in case of emergency.
Naruto finds Greene and develops the same virus that infected Alex Mercer and inject himself with it (this is done to counteract the weakness of his virus (the same one from resident evil 5 where he needs injections to keep up his strength). Once this is done he unleashes Elizabeth Greene to wreak havoc on the Elemental Nations. This is done as a distraction so he can develop the ultimate bio soldiers and wipe out all of mankind.

Whether Naruto still has Kyuubi or not is irrelevant. If Minato and Kushina are still alive, they must raise a twin, and any other children they have, away from the village in secret and return after 12 years. Naruto can't use chakra in this story (he never learned and never learns later on).

The in-between details I leave to whoever wishes to write these, but the events provided must occur, and whether or not he succeeds or fails I leave to the writer's imagination. I would write this myself, but I suck at writing and I really want this to turn out well.

Naruto/Supernatural: Naruto is killed at a young age and Death takes him in. He becomes Death's avatar and wielding his scythe he is sent to kill those who try to escape Death's grip. This story is requires naruto to be killed before he enters the academy. When he comes back he has to be at the correct age. He also comes back without any regard to people, he simply doesn't care one way or another what happens to them. He cannot know everything about the world, he has to hunt down and find his targets. He can teleport to anywhere instantaneously but not know what is there until he arrives.
He can kill weaker/average people by simply being in a place and willing it to happen. Stronger people he can kill by touching them. The strongest (Orochimaru, Hidan, Madara, etc.) he has to kill with Death's scythe.

Naruto/Supernatural 2: Naruto survives the end of the 4th shinobi war but becomes immortal by absorbing the Juubi and outlives everyone. He lives through a great cataclysm that brought an end to the world. The old gods leave and Death and God take over. Thus Naruto grows up in the supernatural world. He then meets the Winchesters at the end of All Hell Breaks loose.
It turns out that Naruto helped Colt build the Devil's Gate and was alerted when it was opened. He hunts down Sam and Dean to ask how it was opened and starts hunting down the demons that escaped. He can do this because of the power of his Juubi Eye, which is a combination of the Rinnengan and Sharingan. But to keep a low profile he has three weapons that he uses. Two modified .45 cal. m1911a1s that he built using the same technique used by Samuel Colt. He also has a single one of his father's tri-pronged kunai made out of a piece of Death's scythe (I will leave to the writer's imagination how it was acquired.).
The guns are able to kill anything, even more than Colt's gun. He made them the next time Halley's comet came. He made the two to be able to kill Angels, demons, etc., anything short of reapers, god, death, Michael, or Lucifer. The knife is only able to kill angels and demons and can possibly kill Michael or Lucifer, and can hurt death or god (pretty much where even they would say that being shot by it hurts like a bitch).
The story follows the Supernatural t.v. show, but with the Winchersters getting their asses kicked less. Naruto will be able to take on pretty much anyone.

Naruto/Push: Naruto develops the ability of Pushers, Movers, and Watchers from the movie Push. He uses these powers in place of chakra. He has to start out small, but grow stronger with time. Able to move larger items, implant stronger thoughts, and see into the future with greater detail and less sporadically. He may also acquire other psychic abilities, but he cannot possess the powers of bleeders or shadows.
Naruto cannot possess the ability to use chakra.

Naruto/Killzone: Naruto is exiled from Konoha by the village council and elders while the Sandaimee is away on a diplomatic mission. He is exiled to a region north of Kaminari no Kuni that is known a region of no return and all the undesirables and the worse criminals of all the elemental continent are sent. Only a small number of people in over a century have ever returned and they all told tales of horendous electricals storms, the air is thick with toxic cases, and anyone who ventures there is affected by an unknown illness and dies. When Naruto is exiled there he comes across people who have built a weak society, where the people are weak from illness and the land is barren. 10 yrs. later rumor of strange creatures and beings along the northern borders of the continent, then a ninja team is sent in an invasion is triggered and all the northern nations find themselves undersiege by an army. armed with strange weapons, and unbelievably advanced technology, the call themselves the "Helghast."
In the story Naruto will take the place of the character from Killzone 3 "Jorhan Brimve Stahl," the guy who's family built the weapons technology for the Helghast. Instead of Stahl, Naruto will come up with the weapons technology and help Scolar Visari build the Helghan nation. Their goal is to destroy the Elementals who had casted them aside and prove their dominance over the elemental nations and their shinobi.
The plot will be the Helghan will be exactly the same as in the video games, this means they do not utilize chakra but technology and weapons. The people in the rising Helghan nation found petricite while digging for usable minerals, but Naruto finds a way to use it. He started by using shinobi's gunpowder to make guns, then from there they build aircraft, tanks, all the stuff from the games.

Naruto/Avatar The Last Airbender: The idea is that Naruto is the Avatar's opposite. The Avatar is meant to keep the balance and Naruto is meant to completely destroy it. The story will go that Madara wiped out he world when it looked like he was going to lose, but Naruto had absorbed the Juubi and survived. Naruto is later confronted by the gods and told the Juubi was meant to be a restart for the world. Whenever it looked like humanity was beyond saving the gods would send out a force to wipe out all mankind so the gods can recreate humanity in a new way that would hopefully work. The "experiment" as it could be called is to give humanity abilities beyond common animals and see if they can attain peace and tranquility on their own. Humanity will also have a single individual born or come at the precipess of peace and unending devastation to be the deciding factor of either their immediate or permanant future. Should this individual die Naruto's job will start and he will wipe out the world. So naruto is now the God's new elimantion force. With this he will be sealed away until the gods need him to destroy mankind, but while he is sealed he can be with his loved ones in the spirit world.
The story starts after Azula hits Aang with the lightning bolt while he is in the Avatar state. After Katara escapes up the cavern Naruto awakens. This can be in the same cave or at some other location. However, before Naruto can start Aang is revived by Katara and Naruto senses it and doesn't begin his mission. Instead he searches for Aang and tells him what the fate of the world will be should he die/the line of avatars ends. Naruto does this because once he is awakened he cannot be resealed until the balance is fully restored or he completes his mission and wipes out the world, and Naruto wants to return to his loved ones as quickly as possible (since taking out the planets population takes months or even years in the first place). So Naruto sees the quickest way to end it is to have Aang fail and making Aang reluctant to use the Avatar State puts him at a disadvantage.
Several events have to occur in the story; 1. Naruto and Aang must fight, with Naruto winning without killing or permanently injuring Aang, to show that defeating Naruto is both impossible and pointless since a new destroyer will be picked by the gods. 2. Naruto's personality must be cynical, harsh and have very little care for human life. While he is the same with his loved ones as he was in his old life, he views the humans created by the gods after his world as different beings. He has to have the position that they brought it on themselves by not appreciating the gifts the gods gave them just like how his own people brought it on themselves. However, he cannot be cruel and relish in their pain, Naruto just wants to wipe them out quickly and efficiently (Unless their total scumbags that the original Naruto would love nothing more than to make suffer, they exist in every place on earth so it wouldn't be too much of a stretch for Naruto to come across some). 3. Naruto must cause and act of devastation; This can include wiping out a town/city, or an army (preferably fire nation, but doesn't HAVE to be). 4. Naruto must also confront the fire lord/azula and tell them the same thing he tells Aang (how he will wipe out mankind if the fire nation succeeds) and face them in a fight where he wins without causing any permanent harm (It cannot effect later fights).

How the story ends I leave up to the writer's discretion, Naruto can either wipe out the world or Aang can save it, but Naruto cannot aid Aang directly.

Naruto's Abilities:
1. Naruto will have the Juubi's eye in both eyes that grant him all the abilities of the Rinnengan and the Sharingan (This includes all the powers of the Mangekyou and Eternal Mangekyou Sharingans). So Naruto will have Ametarasu, Tsukuyomi, Susanoo, Kamui and all other abilities that exist for those two Dojutsu. Also, Naruto's Shinra Tensei cannot be directional. I see it in a lot of Fanfiction where Naruto's shinra tensei can be fired in one direction and not in all directions like it's supposed to. It annoys me and it cannot be that way since it would go against Naruto's lack of care for other human life.
2. Naruto will have jinchuuriki powers. He will have the tailed cloaks, and full beast transformations at his disposal. He will also have his Chakra Mode. He can select each for whatever affect he wants because each has it's own advantages and disadvantages. Naruto will instead of having the Juubi's mind with the chakra, will give back each of the Bijuu's nine minds back and have them provide advice.
3. Naruto will be able to use Sennin Mode. Like I said before everything has it's advantages and disadvantages, this will allow him to find his targets faster.
4. Naruto will be given the Knowledge and Ability to perform any and every Jutsu that ever existed. So if a jutsu was seen in the Manga, anime, or any of the movies it is fair game. This also includes every taijutsu style and all the weapons. You can also include every kekkei genkai or kekkei touta, but how to explain it I will leave to the Individual. Despite this the only ressurection technique that can bring back people from Naruto's universe is Edo Tensei. Still has to use living sacrifices and the people Naruto resserects will either help because they owe him, or he will strip them of their consciousness to keep them from remembering. Use at your discretion.

Naruto is meant to be overpowered in this story. He is a harbringer of destruction and is meant to wipe out all of mankind. He can still be injured, lose limbs, even his head. However, he will be regenerated. For the regeneration type I will also leave to the writer, but I always pictured it like the Juubi's Chakra is first, then the bones, then muscle, then tissue, then skin is reformed, all the while a layer of Bijuu Chakra protects/covers the injured area. The reason for this is when he absorbed Juubi he evolved into a being of pure energy just like the other Bijuus.

Naruto/Semi-Drive Angry crossover:
Naruto works for the Shinigami as "The Accountant". Naruto is to collect those who have disrupted the balance of life and death. Those who have achieved immortality or have the ability or knowledge to perform resurrection techniques. He has the same attitude as The Accountant and the same abilities. He is faster, stronger, and resistant to any damage.

Naruto/Tron Crossover:
Naruto, at a young age, after nothing but pain in his life he searches for a way to escape it all. While having a great mind for technology he develops the idea of inputting himself into a computer. He develops the technology, but is shocked to find that when it works, he is in a place called "The Grid."

Naruto must disappear at a young age, and his family must return to the Village to find that he is gone. After a couple of years, his sister finds the computers and thinking they may be a clue to where her brother is she tells her parents and they launch an investigation. Naruto notes are deciphered and a rescue is mounter to bring Naruto back.

Naruto Modern Weapons:
Naruto is run out of the village at the age of 8. He stumbles upon some designs for modern day weapons; guns, grenades, etc. He then goes underground and is not seen or heard of for 8 years, at least by his name. 6 years after he dissapears a black market arms dealer surfaces, supplying bandit, revolutionary and criminal organization with weapons. Rumor spreads that this arms dealer can get the highest end weapons, from knives to poison gas to anyone, for a price. No one has any idea who he is or what he looks like and no one can tell if he even truly exists. Then, a caravan for the Fire Daimyou is attacked and nearly everyone is killed, the daimyou's niece is kidnapped. The thing about it is that the weapons used were not seen before. It was enough for a small group to take out dozens of samurai and 2 of the Daimyou's Twelve Ninja Guardians with minimal casualties. As Konoha is assigned the mission they find the group who executed the attack and find that this mysterious arms dealer is in fact real and the one selling the weapons. With this new threat they launch a standing order for every ninja to keep and eye and a ear out for any information. As time goes by more and more groups get the weapons and the shinobis are finding themselves overwhelmed. Soon a new Security Group springs up to offer protection, and they have weapons just like the criminal groups, but of what appears a great deal better quality. With this new groups success the shinobis feel they may become extinct since they are losing their business. Come to find out the arms dealer is supplying both parties and his sole intention is to eliminate the need for shinobis entirely and have their way of life go extinct. When Konoha finally manages to see who the arms dealer is, it is Naruto, and he has already amassed an army to wipe out the shinobi nations.
The story has to progress slowly. Naruto will be a lot like the Jackal from Far Cry 2. Naruto will allie with any criminal group that does not use shinobi, and will provide protection for those who do so to steal business. Naruto will amass an army of those who hate ninja for not protecting them, or destroyed their homes in the wars. No shinobi or chakra users can be in Naruto's organization, or be used by it. That is unless it is a distraction or a trap. Naruto will also develop a small number of nuclear weapons, as Uranium and Plutonium will be hard to find and even harder to mine in secret.