Heath Ledger's interpretation of The Joker will be the benchmark performance for a villain in a superhero movie for some time to come, I imagine. He's magnetic to the point that it's hard to see the movie's flaws.
Jeep Swenson's version of Bane in Batman & Robin
is on the bottom. I agree that Tommy Lee Jones' Two Face was basically thrown away, but compared to the next movie's treatment of Bane, Jones was the star of the show.