1. Sephiroth (Final Fantasy VII)
Was there ever any doubt here? Even the hardiest of FFVII haters has to acknowledge Sephiroth's devious accomplishments. For all intents and purposes, he succeeds in his plan to crash a meteor into the planet and destroy the world. Upon discovering his own twisted, manipulated history, he manages to slaughter an entire village, burn it to the ground and smile about it as he calmly walks away. Then, after usurping what's left of a supremely powerful alien entity (his "mother," Jenova), he assassinates the president of Shinra, a company that more or less owns the world. This is all in addition to the fact that his ultimate goal is to become a god. And, of course, he coldly slices down the beautiful and sweet Aeris at her prime. He is truly ruthless, cold and calculating.
That's a lot to swallow. And he pulls it off without a hitch. Sephiroth, unlike most villains in Final Fantasy, begins and ends the game as your main adversary. He's never dumped at the last second for some pinch hitting omni-boss or revealed to be under the spell of some higher being. He's also not a one trick pony like Kefka - Sephiroth may be vicious, but his back story and motives are much richer than the mischievous stylings of FFVI's jester.
And that's the bottom line. Hate him or not, Sephiroth hits all the major points of excellent villainy and still walks away as a potential victor, even when his final form is all but gone.