Mojo Jojo: To tell the truth, i don't know why i like this guy so much. Not that there is anything wrong with him, it's just that he is actually a pretty generic mad scientist-type supervillain. Well, whatever the case, i just luf 'im.
Dr. Claw: A villain with a very generic personality (basically "he is evil!") but with enough cool aspects to him to make the list. Like the mystery that sorounds his identity and physical appearance, the fact the he never gets caught, and his awsome voice.
Hades (from Disney's Hercules): Simply the funniest Disney villain ever. Nah, the funniest Disney character ever.
Sideshow Bob: One of my absolute favorite Simpsons characters. He is both funny and can be mennacing if written correctly. He is also a great way for the writers of the show to criticize pseudo-intellectualism and elitism.
Zorpox the Conqueror (A.K.A. evil Ron Stoppable): Certainly one of the best villains I've ever seen in a T.V. show. He has everything a villain needs to be successful. He has brains, weapons, backup plans, an awesome laugh, and mystical fighting moves. He's everything that Dr. Drakken isn't!
Prospector (Toy Story 2): He's just very entertaining to watch.
Several of my favorites have already been mentioned, but here a few others that I think deserves some recognition:
Johan Liebert: There aren't many characters in fiction that genuinely frightens me, but Johan is one of them. The fact that he's good-looking, soft-spoken and polite only seems to further enhance the vileness of his evil deeds. Deeds that include everything to cause everyone in the orphanage he was at to kill each other, to almost driving a small kid to suicide. Not someone you'd like to meet in a dark alley, or anywhere for that matter.
Feathers McGraw: Quite possibly my favorite character in Wallace & Gromit. Mainly because of the fact that while the character himself sounds silly: He's an evil penguin who disguises himself as a chicken by wearing a glove on his head. Feathers is actually one of the more sinister villains in animation; there's something really unnerving about this guy, perhaps it's his lifeless, starring eyes in combination with the fact that he's facial expression never changes, thus not allowing us to see what he thinks or feels, like Gromit does. In any case, Feathers is a great villain and one I hope to see again some day.
Hank Scorpio: Despite only appearing in one episode, Scorpio is one of my favorite characters on The Simpsons; nice, funny and a really effective villain. In fact, I think he might be a strong candidate for most effective villain ever seen on the show.
Claudandus: A dark villain for a very dark movie. So strong is Claudantus' hate for mankind that he's even willing to kill those of his own kind in order to further his goals. Despite how evil the character was, his death-scene still made me feel sad for him.
Although
I never understood how he was able to talk with his guts spilled all over the floor
I just saw Gentleman Ghost on Brave & The Bold and he's awesome. I even changed my avatar for him. I forgot to mention all of the classic DC villains in my original posts. Other than GG, my favorites were mostly from the Legion of Doom like Black Manta, Gorilla Grodd, Soloman Grundy, etc.