I'm not talking about people who walk a fine line, or who are villains-by-default, though; I'm talking about real, honest-to-god, crush your planet, enslave your women, trigger Armageddon and laugh about it, villains.
So far some of the top contenders are:
Dante (or, in the manga, Father): From Fullmetal Alchemist. These are people who manipulate ENTIRE CIVILIZATIONS just to get the results they want. Dante used everything including the brothers' own resurrection of their mother to achieve her goals. Father manipulated everything since, basically, Atlantis.
Orochimaru, Naruto: Super-warrior shinobi. Master of virtually every technique ever invented. Creator of a particularly disturbing form of immortality. Nobel-prize level research scientist in alchemical and mystical warrior areas. Manipulator of people. Complete and total sociopath. This guy gives me the creeps, and he manages to be somehow cool while doing it. Hannibal Lecter on steroids and with superpowers.
Emperor Palpatine, Star Wars. "All that has transpired here has done so according to my design." For a generation or more THAT WAS LITERAL TRUTH. He screwed up only at the very end. He was also the only really worthwhile thing to watch in the prequels.
Alfred Bester, Babylon 5: Always with a plan that kept you *just* that far from killing him. Always somehow walking away to live another day. A cheerful smile and a total lack of conscience for almost everything.