For me, it would be GLaDOS.
Portal 2 spoiler
She deleted the one remaining human part of herself because it was just too much to deal with. She releases you at the end of Portal 2 as a path of least resistance measure because “killing you is hard.”
What about you, what is your favorite media villain?
Omar Little, The Wire
“I got the shotgun. You got the briefcase. It’s all in the game, though, right?”
I would not have thought of Omar as a villain. The man even takes a stand against criminals killing people not in the game.
I bet the dealers he steals from would consider him a villain.
Excellent!
“Here come Omar!”