Here's my top ten. Spoiler warning, so watch it.
#1: Caius Ballad (FFXIII-2 and Lightning Returns): How many final fantasy villains do you know actually succeeded at whatever their ambition was? Admittedly Caius had to die to do it, but he succeeded in his ambition. Albeit he inevitably forced his own unaging self on everyone else, and effectively condemned the world to oblivion.
#2: Eggman Nega (Sonic Rush series, Sonic Rivals series): Eggman might be an evil genius, but he has limits on what he's willing to do. Eggman Nega of the Sol Dimension, on the other hand, won't pull his punches. If he sees a way to smite his enemies, he will jump at the chance without a second thought to execute said method.
#3: Ganondorf (Zelda Series): Obviously the most well known Zelda villain, whether he's Ganon or Ganondorf, and part of the Triforce bearers. Ganondorf signifies power, and he won't let anything stand in his way of attaining his goal. While he inevitably fails, being sealed away or outright killed, he'll be back somewhere down the line sooner or later.
#4: Emperor Griffon (Dark Chronicle/Dark Cloud 2): A prime example of a misleading villain; You expect him to be some beefy ruler. Instead you get some rabbit person. Not much to say about the ensuing fight. With a clever feint though, he swipes the player character's Atlamillia, and transforms into a form befitting a major villain. At this point he possesses the power to transport an entire palace and it's occupants 1000 years forward in time to the present day. You can understand his motives in that humans effectively destroyed the peaceful life he had, but his decision to completely eradicate humanity is wrong.
#5: Emperor Madoras (White Knight Chronicles): Just when you think the end of the line is in sight, you get a plot twist; the namesake knight of the series was actually the vessel for this Villain's rebirth, subsequently hijacking the body of the pactmaker, Leonard. The ensuing final boss fight pits you against a twisted, demonic form of the white knight, and with the exception of the Avatar Character (A character who never actually speaks, but gains a knight of his or her own), the four other knights are effectively useless, on account of their pactmakers being dead, or unable to call their knights. An ability the player took for granted, stripped away in the blink of an eye.
#6: Specter (Ape Escape): This white monkey might seem adorable, but with his custom made helmet on, he's gifted with superhuman intelligence. Despite being repeatedly bested by the very humans he seeks to usurp, Specter is effectively the kind of villain who doesn't know when to quit. He may have some questionable ideas from time to time, but he usually tends to have a few trump cards in the wings. He also seems to have some form of ESP/Telekinesis.
#7: Liquid Snake (Metal Gear Solid): The borderline insane brother of Solid Snake, and the primary antagonist behind the first Metal Gear Solid game. Being caught in an exploding Hind D and Metal Gear REX wasn't enough to take him down. How he survived each blast remains to be seen, but you can't deny the hand-to-hand duel against Liquid atop REX's damaged body while racing the countdown of a time bomb was a very tense moment for Snake.
#8: Xehanort (Kingdom Hearts series): A time-travelling, body snatching Keyblade Master who isn't afraid to submerse himself in darkness. Not even being split into the Heartless, Ansem, and the Nobody, Xemnas, could keep this scheming old man down for long.
#9: Alex Mercer (Prototype): Intially the Protagonist of the first Prototype game, he's effectively now attempting to bring about a new world whether they want it or not. He just made one mistake in creating his biggest threat. One James Heller.
#10: Jackie Estacado (The Darkness): While technically the "hero" of his story, nothing he does is heroic at all, courtesy of The Darkness turning his foes into a bloody mess; You cross his path, you're already six feet under. You put a hole in his head, he'll be back on his feet soon enough. For your sake, you'd best hope there's plenty of light sources around, or this superpowered hitman will deliver you a swift and brutal death.
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