First some honorable mention. Steve Bartman/Alex Gonzlez, Magneto, Dr Doom, Barry Bonds.
2. Darth Vader - I think he's the most powerful badass in the universe and would be number 1 but as Luke said in Return of the Jedi, "I sense good in you." He'd kick your ass with the light saber or force choke you if you got in his way.
1. The Joker - really is there a better villain? He doesn't play by any rules. He's a maniac. He wants mass chaos. He's pure EVIL! There is no better villain, and is a perfect compliment to BATMAN. The one sad thing is we won't be able to see Heath Ledger's joker in the 3rd Batman movie again. It's the best cinematic performance I've ever seen!
Those are my 5, who's yours?