I had a very, very random idea for a crossover fic today, and, out of curiosity, I checked on FF.net to see if it had been done before and discovered that it had not. I think that it could end up really interesting if done right.
Naruto x Space Battleship Yamato (a.k.a. Starblazers)
Personally I could really see this happening:
Naruto: Ooh! Captain! Can I fire the Wave Motion Gun? Please?
Captain Okita: Naruto! For the last time! YOU CANNOT FIRE THE WAVE MOTION GUN!
Naruto: Dammit! You're no fun...
Also, Naruto making his own miniature chakra-powered Wave Motion Gun.