343 Guilty Spark is not your typical villain, since he is a mix of good and bad character types with a weird sense of humor. It's not his fault he wants to eradicate life in Halo's Universe--he was programed to perform this task no matter the costs.
He is very polite and hard to hate, but he has his flaws since he is technically insane after all those years in solitude.
GLaDOS, from the Portal series, is a very interesting (psychotic) character who just wants to test your survival skills and abilities. She goes back and forth in being evil or good towards you, but she will never miss an opportunity to make fun of you or your situations.
It is hard to place GLaDOS on the evil podium, because her agenda is only focused on you following the testing path - something you will always disregard to piss her off.
Heart of the Swarm has a great villain with a very diabolical plan in action. Emperor Mengsk, a former revolutionary against the Terran Confederacy, ascended to the Dominion Throne by betraying his trusted allies (Raynor, Kerrigan, and Duke). He even generates another super-villain named Queen of Blades (when Kerrigan was left to die on the Zerg infested battlegrounds). So far so good, but unfortunately, he is nothing more than a coward hiding behind a huge armed force, never to confront the player directly.
Though he is frequently mentioned in the previous games, he was easily forgotten since Kerrigan and Duran were a more imminent threat to the Starcraft nations.
In Mass effect 2, the Human Reaper is the big bad daddy feared by everyone. He is presented as being part of an awesome and terrifying race of destructive sentinels, which endangers all existing life.
Then, the final boss battle begins and you discover how stupidly easy it is to defeat him. There is no other way to put it, but this boss looks like a retarded version of an oversize Terminator.
Alduin is the dragon of all dragons in Elder Scrolls V: Skyrim. He is bad ass, has a cool voice and accent, and is a sheer power that no one can match.
Well, that would be true if they would write a book about him, but in the game he is nothing more than another oversize dragon with a higher HP bar. There is nothing special about his attacks since he still flies around to spit fire, and then lands on the ground for some melee biting, only to be defeated in the end by devastating blowing-hits from your dragonborn.
