Hmmmm... let's have a bash at my own list. No guarantees I'll make ten, though.
SHODAN (system shock 1 and 2): The AI who would be God. What more can really be said about SHODAN that hasn't already been said elsewhere? She's smarter than you and she knows it. She delights in being sadistic towards you, and her evil schemes involve taking over the whole of reality. What's more, you do it for her. Master manipulator and evil genius nonpareil.
Darth Treya (Knights of the Old Republic 2): Darth Treya continues the manipulator theme - a mentor of the harshest kind, she's your companion throughout the game, offering double edged compliments, harsh criticism, and constant disappointment. Then she tries to kill you.
GLaDOS (Portal): A fairly obvious choice here, Portal's insane AI is a benchmark for comedic writing in videogames whilst still managing to be a menacing villain.
Arthas (Warcraft 3, Throzen Throne, and Wrath of the Lich King): For most of Warcraft 3, you -are- Arthas, witnessing firsthand his slow slide into madness, and eventually rebirth as the right hand of the Lich King. You tear down your own kingdom, destroy the city of Dalaran, and raise yourself up to the status of Big Bad of the World over the course of a game and its expansion pack. Too few games let you actually play as the villain in a meaningful way. What's worse for Arthas is that he basically has no other choice. His fall is a series of forced circumstances in which he arguably makes the best bad choice possible. The culling of Stratholme might have been a sick thing to do, but it's better than facing them the next morning as an army of the undead, surely?
Loghain (Dragon Age): I'll try and avoid spoilers for this choice, since it's still a fairly recent game - but Loghain is a villain that at least makes sense. Everything he does is for a greater good, and whilst he might be misinformed, machiavellian and utterly dickish, at least his heart's in the right place.
Karras (Thief 2): It's the voice that does it really. Thick with speech impediments of every flavour, Karras is the mastermind behind a steampunk revolution that sees the world in which Garrett, Master Thief lives in turn into a hive of robotic monstrosities, all speaking with the lisping, pathetic voice of their creator.
Prince LaCroix (Vampire the masquerade: Bloodlines): Oh boy. This guy is fantastic. Watching him go from controlling Prince to obsessive madman over the course of the game is beautiful. His moods are loaded onto roundabouts and hurled into a centrifuge, one minute he's giving you money for a job well done, the next he's trying to kill you. Then he's declaring you his most loyal follower and sending you off to get torn to shreds by werewolves. (not necessarily in that order.)
Then he explodes. Happy endings for all!