The thing that sets apart great comic books from the rest are the quality of their villains. While superheroes are stuck playing the boring good guy know-it-alls, villains get to plan the crazy schemes, blow stuff up, and cause the kinds of havoc and destruction that makes comic books work. 850,000 votes are in (check out the results here),
Doom should be #1. You didn’t mention that during a fight with Iron Man, the two of them were sent back in time to Camelot, and Doom decided to team up with Morgan LeFaye, raise an army of zombies, and try to kill King Arthur.