I'm a Joker fan, but since he's a clear favorite I'll go with Prometheus. I love him because, to me, he is the Anti-Batman: Bruce's parents were killed by criminals; Prometheus' parents were killed by cops. Batman punishes those who break the law; Prometheus targets those who uphold it. I actually hated that he got killed by Green Arrow during Justice League: Cry for Justice (pre-New 52) but maybe he will return (a successor perhaps?) Add to his resume the fact that he clowned the JLA and almost got away with it, and we're talking about one of my favorite Batman villains.
Close seconds: Mr. Freeze, Two-Face, Riddler, Killer Croc, Hush