ideas I have:

Victory at the Valley: An AU Naruto Story where Naruto won at the Valley of the End and brought back Sasuke back. Sasuke has now spent three years in jail when Naruto returns from training and gets rid of his Curse Mark. Now Sasuke must take his own steps towards the path of redemption...

The World Ends with Lelouch: Lelouch as we all know, dies during episode 26. He then wakes up in Shibuya with no memory and forging a pact with this strange redhead named Shirley...

The World Ends with Kamina: What happens when the guy who kicked off Tengen Toppa Gurren Lagann wakes up in Shibuya?

The World Ends with Shinji: Yup thats right- Shinji Ikari wakes up in the Reapers Game- and his partner is Asuka of all people, and given the Games tendency of psychological examination and testing its players, what will happen to them?

Fullmetal Geass: Ed is dragged into the Gate- then the God inside of it decides to drop him right into the middle of Britannia's invasion of Japan allowing him no Alchemy. However during the first episode of Geass he gains it back by making a pact with CC who unbeknown to him has also made a pact with Lelouch- the girl is smart she knows not to put all her eggs in one basket...

Code Kamina: Kamina receives the Geass from CC instead of Lelouch, AWESOME ensues!

Tengen Toppa Naruto: What if Naruto watched too much Tengen Toppa Gurren Lagann as a child? This happens...

Naruto Genesis Evangelion: Team 7 Wakes up in the NGE verse- and now they have to save it from the Angels- but their teamwork is bad as ever...

Neon Genesis Naruto: Shinji, Asuka and Rei wake up in Konoha and must find a way of working together under the shinobi's harshest administrations...