Who is your favorite villain of all time? You can choose anyone, from anywhere--television shows, comic books, movies, novels--they're all fair game.
Personally, my favorite has got to be the Joker, from Batman. I couldn't tell you exactly why, but I think it's the (quite literally) insane and unpredictable way that he operates, with no loyalties to anyone but himself--even amongst the other villains he encounters in Gotham.
My favorite reincarnation of the Joker is the one played by Mark Hamill (Luke Skywalker is the Joker! Ruuuun!) in Batman: the Animated Series. Mark Hamill also plays the Joker in the Arkham Asylum video game, and does a wonderful job there, too... I'm not quite as fond of the "disheveled" Joker as I am of the "impeccable" Joker, though.