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?
Hex and Daemon from Reboot are both underrated. Hex has genius visual design for the limitations of the technology. And for a kids show, Daemon is very likable, which always makes a villain more compelling.