Beginning notes: Ganon and Ganondorf are two different incarnations of one spirit. Though together they are stronger, they can live apart. Just thought I would clear that up before I start this, to save questions after the story.
In the Beginning.
Obviously, we all know the first event in this timeline. That is the Goddesses creating the land of Hyrule as well as the other lands scattered about the LoZ world. (E.g. Termina.) After which the Goddesses left parts of themselves behind in what is known as the Triforce, the most sought-after relic in the LoZ world. What followed was a "Great War" so to speak, the end result of which would determine which land would control the Triforce. The war raged for centuries, but just before the end of it, a woman and her child fled for their lives. They took refuge in a small section of Hyrule, known as Kokiri Forest. The woman pled with the forest's caretaker, the Great Deku Tree, to take care of her child as her last dying wish until he finally agreed. This led up to the events of the LoZ: Ocarina of Time. After several small quests leading up to the retrieval of the Master Sword, the boy was sealed away for seven years in the Temple of Light, before he was finally ready for the battle against the King of Evil; Ganondorf. This is the start of the time paradox that would later split the timeline into two parts. After several more quests, the Hero of Time battled Ganondorf, defeating him and killing his beast incarnation Ganon.
The Adult Timeline.
Now comes the timeline split, I will start with adult timeline. After Ganondorf's defeat, he is sealed away in the Dark Realm and the Master Sword is sealed back into the Temple of Time, all before Princess Zelda sent Link back to his time. With Ganondorf sealed away, time passes normally, until centuries later. A distant ancestor of the original Hero, passing on the name of Link, is sent on a quest to stop Ganondorf from breaking through the gate of the Dark Realm. This starts the events of the LoZ: A Link to the Past. (Note; the Master Sword was put away, therefore it still exists.) During this quest, Link successfully keeps the Dark Lord from breaking his seal, keeping order in Hyrule. At the end of his quest, the Hero returns the Triforce to Hyrule castle safely, causing it to warp him to a far off, yet troubled, world. This results in the LoZ: Oracle of Seasons and LoZ: Oracle of Ages. During these two quests, Link kills the resurrected beast incarnation of Ganondorf; Ganon, who was brought back by the Gerudo witches Twin-Rova. Centuries pass and Hyrule stays surprisingly peaceful until Ganondorf, who has gained back his full power plus some, breaks his seal. But there is no Hero to stop him. To keep the King of Evil from once again corrupting the land of Hyrule, the Goddesses flood the great kingdom out of desperation. Using almost all of his available power, Ganondorf manages to keep a barrier over Hyrule, keeping the Great Sea from washing it away. This is where the LoZ: Windwaker starts. The newest Hero races to collect the pieces of the Triforce of Courage, scattered along the floor of the Great Sea, before Ganondorf gets them. Following this is a battle, resulting in Link piercing Ganondorf with the Master Sword which turns him to stone. So now we have no Ganondorf, no Ganon, and no Master Sword. Years after this event is the start of the LoZ: Phantom Hourglass. Not really much to say about this one other than it is a filler in the timeline, leading to the next event. Said event would be the start of the LoZ: Link's Awakening. Blah blah blah, Link is lost at sea, he awakens the Wind Fish, and now we're at the end of the adult timeline. This is it for now, at least until the LoZ: Spirit Tracks comes out in December, 2010, as it takes place after Link's Awakening in the timeline. (SPOILER!!! The sea is drained for some odd reason lol, and it is confirmed this game is a century after Phantom Hourglass.)
The Child Timeline.
Okay, back to Ocarina of Time and the child timeline. This would be my alternate ending, and in this case, Link is unable to defeat Ganondorf. So they take the lazy-ass way instead. Zelda sends Link back in time, where he goes to child Zelda and tells her about the impending doom, i.e. Ganondorf taking over the land. When the king finds out Ganondorf's supposed "loyalty" is fake, he sends him to Gerudo desert to be executed by the sages. But.. their swords are unable to kill the King of Evil, a job only the Master Sword can do. Instead they just open up the gateway to the Twilight Realm and banish him to there instead. With Ganondorf being sealed away, Link goes off to the Lost Woods to search for Navi, who had disappeared after he was sent back in time. While travelling in the Lost Woods, Link encounters the Skullkid, who is under the power of Majora's Mask. The Skullkid steals Epona and the Ocarina of Time and Link chases him into Termina, there you go; now the LoZ: Majora's Mask is started. Ganondorf is currently sealed away in the Twilight Realm and Link isn't in possession of the Master Sword, so nothing serious enough to drastically influence the timeline happens here, just passing time I guess. (Nothing is officially said, but I say Link went back to Lost Woods to search for Navi again after Majora's Mask.) Centuries after this quest, Ganondorf gains immense amounts of power and somehow escapes the Twilight Realm, throwing the events of the LoZ: Twilight Princess into play. After killing Ganondorf, all is normal again and the Master Sword is put back. (Same old, same old) Years and years pass, leading up to the LoZ: Minish Cap, in which the Master Sword is destroyed. The remains of the Master Sword are then re-forged, forming the Four Sword. Obviously, the LoZ: Four Swords is next, (DS and GameCube versions.) During this quest, beast Ganon is sealed inside the Four Sword. Later down the road, Ganon breaks the Four Sword, ultimately freeing himself, where he comes up with the plot to kidnap the current princess. This quest would be known as the original Legend of Zelda. During said quest, Link eventually battles Ganon, killing him with a Silver Arrow and freeing the princess. All is well, but not really. (It's Zelda, of course not really XD) Now comes the LoZ 2: The Adventures of Link, where Ganon's minions try to bring him back by spilling the blood of his killer on his ashes. They are… obviously unsuccessful, like I said, it's Zelda 8D. And this ends the child timeline for now.
Ending notes: I'm aware of a current Zelda quest in the making, and when it comes out in 2010 or 2011, I will update my timeline and put it in there. I'm guessing it will take place a bit after Twilight Princess, but who knows? And also the same for Spirit Tracks, which I'm 100% sure comes after Link's Awakening in the adult timeline.
Additional Bits.
During the LoZ: Twilight Princess, after you do a Howling Stone in wolf form, pay close attention to the technique teacher. He appears to be a Stalfos under the armor that he wears. He says himself that he used to be a Hero himself, and at one time put Ganondorf away. On this timeline, (the child timeline,) there was only one Hero of Time before the current Link, and that was our Ocarina of Time/Majora's Mask Hero. It was said in Ocarina of Time, that anybody who dies in the Lost Woods turns into a Stalfos, and it's a coincidence that's where Link went after beating Majora's Mask. Is it possible that Link somehow died in the Lost Woods and is teaching the new Hero his techniques? In addition, pay attention to his weapons. The Stalfos teacher seems to be using a dirty Gilded Sword and Mirror Shield… Both weapons that you retrieve in Majora's Mask… Coincidence? I think not, but that's my opinion, what do you think?
So thanks for reading, did you like it? You could just hit that little review button there and tell me… But anyways, yea I really did my homework on this one, and I think it all ties together. (Nintendo says it doesn't, but what the hell right?) If you have any questions or would like to add anything, feel free to e-mail me at masta_big_ with the details, and I will update it if it fits 8D. But yea, reviews guys…