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.
Has to be the Illusive Man from Mass Effect, it's his persona, I could listen him talk all day long.
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.
Rrrrr-obotnik! Only because of the tv series portrayal to be honest.
Kefka and Sephiroth
Bael'Zharon from Asheron's Call - was a GM controlled main villain as part of the game's most memorable story line.
"There are two types of guys in this world. Guys who sniff their fingers after scratching their balls, and dirty fucking liars." -StylesClashv3
"Elo Hell is where the Ego is greater than the Elo." -Bystekhilcar
Jon Irenicus from bladurs gate 2 and Luca Blight from Suikoden 2.
I am rather fond of Ansem from Kingdom Hearts. Though that was because I couldn't stop laughing at the ship he was on at some point during the fight. It looked like a giant penis. Given the past penis sightings in Disney stuff... I giggled.
I also really like all of the old gods from the Penny Arcade series. Any boss that gets me to break the spacebar on my keyboard during the fight... He is worthy of my admiration. Granted, it was Gabe's special that caused me to break the keyboard, but that is beside the point.
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
Prince Lyon in Fire Emblem Sacred Stones was pretty damn evil despite being controlled by an evil force.
Also Lllender Twem, and the Queen in Final Tactics Advance.
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.
Oh and also Mehrunes Dagon from Oblivion