So hard to pick. I think I have some biases. I'm also picking on potential too.
1. William Dafoe - Probably my number one, until I think of something else. He has a good 'character face', which is fitting of an evil person. I think his portrayal of the Green Goblin was awesome too.
2. Tilda Swinton - One of my favourite actresses. She should appear as a villain more. She was awesome in Constantine and Narnia.
3. Hugo Weaving - I think he's better than the movies he has appeared in. Hopefully he gets a good role soon.
4. James Earl Jones - I liked his look in the Conan movie, and his voice is awesome. I think he had the potential to be a good villain, had he got a decent role (and not just a voice, eg: Darth Vader).
Special Mentions
Gary Oldman - Tempted to pick him merely because the Fifth Element is one of my favourite movies. I wish there were more movies with that look and feel.
Robert Patrick - A has been? But he played the bad guy in Terminator 2 very well.
Tom Cruise - He'd play a good villain, because we already hate him.
Christina Ricci - As a child actor, I reckon she'd have been an awesome evil character. Wednesday Addams, enough said.
Julian Sands - Purely for his depiction of the title character in Warlock.
Julie Carmen - Fright Night, part 2. Flash in the pan.
Can't think of anyone else for now
. Yes, there are notable exceptions, but I have my reasons =p.