I would not hesitate to say that TDK's Joker is the best film villain in the superhero genre. But if we were to look at film villains as a whole, there are a few I'd put above him.
Norman Bates
Hannibal Lecter
Jack Torrance
Walter Kurtz
Darth Vader
Anton Chigurh
Hans Landa
Also, it was a very small role, but I have a soft spot for Delbert Grady. Philip Stone is so damn unnerving in that bathroom scene.
"My girls, sir, they didn't care for The Overlook at first. One of them actually stole a pack of matches and tried to burn it down. But I corrected them, sir. And when my wife tried to prevent me from doing my duty, I corrected her."