Vergil from Devil May Cry 3. Probably the hardest villain to fight in any game and also the coolest with his crazy powers. Also don't forget about Bowser.

I'll have a different answer once I've had a chance to think about it. But right now I'm going to say Magneto. Mainly because he's a villian, but not a cartoonish stereotype. He's an intelligent man who has seen awful things and has come to the conclusion that it's what he has to do.

the freaking dog from Duck Hunt. OMG http://www.cyberiapc.com/flashgames/duckhunt.htm

Kefka - This guy is not a villain. He is not a super villain. He is a raving frigging psycho path. He starts off as a weird guy in the high-ups in the military. His psycho reign starts when something is started about solving a rebellion problem in a village... Let's poison the water. Kehehehehe. Let's create the power of the gods and become a god myself!!! Kehehehehe. Now that I'm a god, Let's make the world how I want it!!! Kehehehehe. Kefka is not right in the head. I say he is the best Villain ever... from anything. I would love to play a FF6 knock-off *AS* Kefka. (it would be twisted as the goal would be to do psycho things to innocent people) But hey GTA4 sold like hot-cakes, and your job is to steal cars... That's kinda psycho! I'd have to say the Main Character off GTA4 is good as well. Cant think of any villains that have done more destruction than him.