Here are some of my favourites:
Iron Trek - Star Trek / Iron Man AU crossover (Kirk/McCoy)
Kirk creates a suit of armor, but his best friend McCoy doesn't know about it. Bones works for the government and his chief wants to know who has created this thing called Iron Man.
500 Days of Sulu (Sulu/Chekov)
Another Place and Time AU (Kirk/Spock)
James T. Kirk is an ordinary guy from a small town.
What are your favourites?