hmmm... i don't think i could say i have a favorite. every time i think one was going to exceed the others, they'd do something to disappoint me. you see i believe the best villain is a hero, more specifically; someone who has a good reason for what they're doing or even better a morally good end goal to justify their actions. the reason i think this is because it seems more realistic, no one does evil things for the sake of being evil. every person does what they thinks is right, what'll improve the world and such. and the baddies used the same thoughts, but came to a different conclusion.
that's why i always liked anime villains since this happened more often in them, but the best example i could give for a great villain would be Magnito; he was an "ends justifies the means" and "at all costs" kind of guy. hell in the original comic they planned for him to succeed professor X, but was shut down due to it removing the main enemy and concluding the series. the comics were selling well, they didn't want to screw it up. though the entire x men were a re-skin of the civil rights movement. professor X was Martin Luther King Jr. and Magneto was Malcom X.
some others would be like Kira from Death Note or Lelouch from Code Geass. they were the main protagonist, but they also embody the core of what i believe a good villain should be, heck a slightly different writing of either of them would of made them the villains.
the other trait i like in a villain that sticks out is arrogance, i don't know why but it's appealing in them, but insufferable for anyone else.
anyway that's my thoughts on the matter.