i kind of like the tragic figures like magneto, vegita, juggernaut etc. but i can't really call them villans either. That being said, herre are the best i could come up with (and i'm assuming you mean fictional);
Joker-in the right hands the best villan ever created
Scarecrow (dc)-so much potential
Starscream-come on he's fucking classic
shit i can't really think of others.