LOUD NOISES!!!
OT: Um... I'm sure it's been said, but I'm gonna say Joker. Notable mentions are: Starscream, GLaDOS, Magneto, and Team Rocket. There are others I could mention, but I don't want to be here all day.
Joker - Perfect villain in almost every way. Do I really need to explain?
GLaDOS - Computer running a facility goes crazy and kills people? It even has a human-like personality which makes it even scarier.
Magneto - I love a villain who believes his/her actions are in the right. Magneto is the best example as he believes mutants are superior to man. It's just a different way of dealing with Mutant-Equality.
Team Rocket - From the games, Team Rocket has been the only Pokemon Team to earn my respect. Which is why it's always sad to see the organization fall apart in Generation 2. If the franchise had stuck with them, I think it would have been stronger for it. All these new teams can't even compare to these guys. Plus, for a while, they were actually kinda funny in the anime.