3. Spider-Man and The Punisher
Now, this is one of the more obvious crossovers for comic fans, but the casual movie public might not understand. You see, technically The Punisher got his start in Spider-Man comics, and he continued long after he got his own series. Its really one of the greatest odd couples in history. You have the teenage (sometimes) Spider-Man, the eternal everyman just trying to do right with his super abilities; and you have a war veteran who likes to shoot bad guys in the head. One likes to defuse tense situations with jokes; one likes to shoot bad guys in the head. One has super powers; one you get the idea. The set-up for a movie is right there in the comic books. The Punisher arises as a vigilante who kills gangsters and criminals. Spider-Man is wanted for the murder of Norman Osborn (The Green Goblin) via some classic misunderstanding hijinks. Thus, The Punisher steps in to kill ol Web Head. They made nice later, but it was fun while it lasted. Of course, with the Spider-Man reboot we may have to wait awhile for this storyline to be set-up, but its an easy choice as a B-story down the line if nothing else.