How about ol' "Nosferatu" hisself, Scorpius? Quite manipulative and seems to have an ace up his sleeve at all times. Like a cockroach, just when you think he's squashed, he'll pop up someplace else. (Doh! Figures I'd wait too long before hitting submit) To a lesser extent, Commander Bailar Crais is equally obsessive compulsive as a villain, all of which started from a simple accident that led to brotherly revenge.
Hrm. Farscape has a few other villain possibilities like that Nebari chick that had Durka mentally cleansed (same episode as Chiana's first appearance) or the semi recurring villain Maldis. There's also Commandant Cleav, er, Grayza. She'd be the seductive black widow mastermind at the center of a web.
What about Mister Evil? That's DOCTOR Evil. Didn't spend 6 years in evil medical school to be called Mister, thank you very much.
There's also Magus from Chrono Trigger as well as his former lackeys Ozzie, Slash and Flea. Ok, they were rather incompetent.