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?
The great thing about Dukat is that he frequently finds his own humanity. You keep thinking that this time he’ll do the right thing and start his path to redemption, but he never does. He always chooses to do the wrong thing even though there’s clearly good in him and you’re always disappointed and even surprised when it happens. He’s like the anti-Zuko.