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?
Handsome Jack.
Best hero to villain in a game yet. Plus dude had charisma for days so even though he was a clear cut asshole you couldn’t help but love his antics.
Butt Stallion is an amazing throwaway joke, just so much thought put into even the stupid stuff.