I'm not the biggest fanfic, er, fan, but I once ran across on while looking up something else which had a rather intriguing premise: dropping the Demi-Fiend (player character from Shin Megami Tensei: Nocturne; a kid who survives the end of the world, becomes a demon, and gets to decide what the new world will be like) into the world of Harry Potter.
The fic itself didn't make the most of the idea, but I still found it amusing because it's kinda like dropping a Balrog on the Smurfs. Demi-Fiend is just on a totally different playing field in terms of raw power.
And then there was that Star Trek:TNG / X-Men book I read. No, seriously, this was a real, published book.
Anyway, probably the most twisted crossover notion I ever had (and I've had a bunch) is:
Grave of the Firefly
This could actually be made into a serious and touching story about orphans from the war for independence, with or without the Serenity crew getting involved.
Or it could be an utterly ridiculous insertion of two of the most tragic figures in all animation into a Firefly setting, because we hate art.
Other notions:
Buffy/Disgaea (Laharl pops out of the Hellmouth and starts running rampant. What's a Slayer to do about a loudmouthed prepubescent demon lord with enough power to single-handedly crush a space fleet?)
Ben 10/Killer 7 (The Smiths are on a mission, and Ben keeps getting in the way. How long before the showdown between seven trained killers and a superpowered little boy? Taking all bets!)
Pokemon/Fallout (In post-apocalyptic Japan, the technology exists to control the mutated creatures wandering the landscape. Besides their use for labor and protection, these beasts are pitted against each other in the arena. The League which runs the show under the watchful eyes of the enigmatic Elite Four, takes a cut of all bets. As long as you win, all your dreams come true. Lose, and you're monster chow.
Ash, orphaned by the Elite Four, is determined to rise in the ranks and become king of the arena - then overthrow the Elite Four and take the reins for himself. With his beloved radioactive mole rat and faithful companions, such as the lecherous ghoul Brock and the sassy super mutant Misty, he just might succeed.
"Wild Deathclaw appeared"
"Go! Mole Rat!"
"Deathclaw used Slash!"
"Mole Rat was eviscerated!"
...or not.
