Glad0s, Wheatley, and Handsome Jack.
1. Shodan, amazing game, amazing villain.
2. Kefka, another great villain, and the only voice acting ever in any final fantasy that was even mildly tolerable.
3. Gunther Hermann, a real high point of deus ex for me, well characterized with your existance being a walking symbol of his obsolescence.
4. Metal Gear Rex, screw Liquid, Rex is the star of MGS.
5. Prinny, just because dood.
Ultimecia form FF VIII, she herself and when she was controlling Edea.
Rilix (and Vandals in general) in Shining the Holy Ark.
Mortanius and Moebius in Blood Omen Legacy of Kain.
Nice to see someone played this game. It was truly ominous to have your young characters to go into that cave only to find this... Oh it was quite a time ago, I don't even remember much about this game, time to replay it soon. Lou-Fu in BoF 4 was also quite an interesting antagonist as well.
Rrrrr-obotnik! Only because of the tv series portrayal to be honest.
Kefka and Sephiroth
Seymour and Jecht for sure. They were great characters and I don't think I ever had so much satisfaction watching them die.
Followed by the Lich King. As testament to my love of Arthas, despite him being a whiny punk, I have the Arthas/Sindy Megablocks set.
Jon Irenicus from BG2.
Jon Irenicus from bladurs gate 2 and Luca Blight from Suikoden 2.
Grunhilda from Banjo Kazooie,
Bowser from Mario,
Diablo from Diablo Series,
Lich King from Warcraft Series,
Ganon/Ganondorf from Zelda.
All I can come up with now.
Loghain Mac Tir from Dragon Age Origins is probably one of my favourite "villains", however he is more of an anti hero suppose.
Great character & voice acting nevertheless.
Persona 2 final.
Guess who´s that!
Yes its him.
And his boss
Nyarlathotep
Surprised no one mentioned The End from MGS3, he even won a few years back some best boss polls iirc. That boss fight was insanely stressful and patience-testing.