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?
If favorite is a villain whose motivation was pure and got perverted by his obsession and still awesome:
General Woundwort
If favorite = one i hate the most, it is a tie between:
Joffrey
Ramsey
If favorite is a villain who is cool as hell it is a tie between
Voldemort
Hans Gruber