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No one's mentioned Dr. Wily? Come on now...

Another vote for Karras from Thief II: The Metal Age as well.
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Thiefer: No one's mentioned Dr. Wily? Come on now...

Another vote for Karras from Thief II: The Metal Age as well.
Just vote for Kirby I mean comeone Kirby is freaking evil!
And Papu-Papu from Crash Bandicoot! :D
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keeveek: And Papu-Papu from Crash Bandicoot! :D
No, we should vote for Tiny from CB! :D
I'd pick any of the antagonists from Xenogears.
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Adokat: I'd pick any of the antagonists from Xenogears.
Hi-five!
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Adokat: I'd pick any of the antagonists from Xenogears.
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Taleroth: Hi-five!
:D Right back at ya!
The obligatory joke answer: The Grinning Colossus.
Seriously, though, I'd second Kefka. He pulls off the chaotic evil trope - destroy the world, just to watch it burn - pretty well; by the time you face him, you have reason and motivation to loathe him. You actually see him doing evil - up to, and including destroying the world and remaking it in his image - as compared to so many 'I'm the boss of all those mooks who were trying to kill you' final bosses. Seriously - what did Mother Brain ever do to you? She's a brain in a jar! You crash land on her planet, raid her storehouses, hunt down and kill her most trusted guards, and when you finally get to her, you break open her life support system and fire piles of missiles into her. The rest of the Metroid series is just about revenge for destroying her initial home!
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Palehorse: My first thought was Irenicus from BG2. I loved his dialogue and he was a deliciously creepy and sadistic baddy.
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MartectX: Irenicus.
Sarevok from BG1. I always liked BG1 better than BG2, and besides, you get to have Sarevok on your side in BG2!
elminster in BG1, extremely annoying, popping in only to utter some nonsense and disappear followed by my arrows and spells, sarevok is nothing compared to him!

Also, GlaDOS and Shodan, never felt more threatened in any other game
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dr.zli: elminster in BG1
Elminster is a prick
Khelben Blackstaff (Eye of the Beholder) is a prick
Lord Order (Dungeon Master) is a prick
Eldrad Ulthuan (40K) is a prick

Notice a pattern? Wise and powerful magicians are often manipulative bastards who get other people to do their dirty work.
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dr.zli: elminster in BG1, extremely annoying, popping in only to utter some nonsense and disappear followed by my arrows and spells, sarevok is nothing compared to him!
Elminster is just trolling the PC, he isn't really a 'villain' per se. But, yeah, he does do a mighty fine job of it! :)

However, using your reasoning, I'll have to change my answer:

The children of little Lamplight in Fallout 3. They troll, insult, and waste the PC's time, but can't even be killed with console commands. Maybe there is a mod for it allowing children to be killed in FO3 now. That would almost make me want to re-install the game.
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Krypsyn: The children of little Lamplight in Fallout 3. They troll, insult, and waste the PC's time, but can't even be killed with console commands. Maybe there is a mod for it allowing children to be killed in FO3 now. That would almost make me want to re-install the game.
There is but you won't find it on the Nexus as Robin banned child killing mods. For obvious reasons really.
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Delixe: There is but you won't find it on the Nexus as Robin banned child killing mods. For obvious reasons really.
I still wanted to face-shoot that one little girl in the face once, then reload a previous save. I blame the writer that gave her all the venomous lines, bu no option to spank her and tell her to behave (for negative Karma, even). But, nope, not even that. ;)
Jack Thompson?

Hitler... I mean "Master D" from Bionic Commando? Kane from C&C? Ad Advis in the Quest for Glory series? Game balance in StarCraft II?

I want to say Jon Irenicus from Baldur's Gate II, but I'm going to go with The ghost pirate LeChuck instead. (Monkey Island.)