I suppose there are three for me.
#1 - Londo Mollori from Babylon 5, specifically seasons 2-4. What I love about him is that he is not your typical sociopathic bad guy. He's not insane, or the living embodiment of evil, or any of that. Instead he is actually a very sympathetic figure. In the first season we come to know him in a positive light. He is a screw-up, a loser, a washed up diplomat in a backwater post. At one point he describes himself as "the odd man out", and it sums him up to a tee.
But as the first season ends, the Big Bad makes him a deal, an opportunity not only for his own personal power, but also to return his now weak and decrepit nation to its once great status as a powerful empire. He takes it. He knows what he is doing is wrong, he feels guilty for the millions who die because of him. But he just cannot stop himself. This is his chance, and he is going to take it, no matter what it costs his soul.
I also like that Londo is not a super-powered tough guy. He is a thinker. When he puts his mind to it, he is simply a genius. Ironically he is at his best when it comes to murdering his allies. No one manipulates people like he does, and he does it with such style that you cheer for him. It also helps that his allies are much further along the true evil scale then he is. And the Rock Cried Out, No Hiding Place, is a wonderful example of this. Not to mention what he does to Morden and the Shadows.
#2 - Scorpius from Farscape. Wayne Pygram (who also had a minor appearance as Governor Tarkin at the end of Revenge of the Sith) plays the stock evil overlord to perfection. I think what ticks for him are his motivations. He is a half-breed Sebecean/Scarran, the two biggest, evilest races in the galaxy. Also the most physically incompatible. The Sebeceans are very similar to humans, but have a serious problem with heat, which can kill them. The Scarrans on the other hand, are made for extreme heat. So the hotter he gets, the more raw power Scorpius gets from his Scarran side. And the more he comes to death thanks to his Sebecean half. Because of this he has to wear a special cooling suit, and even worse, cooling rods inserted into his skull, which have to be replaced on a regular basis.
He came about from a genetic engineering experiment by the Scarrans, and spent his early life as a Scarran lab rat. Until he eventually killed his keeper and escaped. He joined the Peacekeepers - a Sebacean mercenary empire - to get his revenge on the Scarrans. His interest in the protagonists is the wormhole technology that John Crichton has. The Sebaceans are vulnerable, and the Scarrans on the verge of finding out and launching an all out war to annihilate them. Scorpius needs the wormhole tech to turn the tide. He will do anything to get it, even putting a clone of himself inside John's brain.
He is tons of fun, because while being very powerful and ruthless, he has some serious weaknesses as well, along with some good motivations.
#3 - Darth Vader. Pretty much a cardboard supervillain. But he is the first bad guy I ever saw who was cooler than the heros. He wins for me simply on that coolness factor. James Earl Jones' voice is of course a big part of it. But his lines are just priceless. "Apology accepted, Captain Needa." is still one of my all time favorites. Along with "I find your lack of faith disturbing." I think he killed more Imperial soldiers than the Rebellion ever did! Which I liked, because it showed the real face of the dark side: unbridled destruction.
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