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 for no other reason than to have a bit of a different answer:
Raboniel from Rhythm of War by Brandon Sanderson
Her interaction with Navani made for some VERY good chapters
Incredible character, always had me guessing at her true motives and alignments. RoW was just an amazing installment in the series