This one is a bit tougher. There have been good villains in games I’ve played and ran. A Lovecraftian toad-god monstrosity from the first campaign I ever played is the first to come to mind. An ancient, world-devouring vampire we totally set free (the GM didn’t think we would open his coffin. We, however, wanted to create a distraction, and that coffin was just so tempting). There have been terrorists turned allies, mages attempting to reshape the world, time itself, body-possessing aliens, and countless others.
After over a decade of playing, I’m not sure I have a favorite villain. Usually, my favorite part about a villain is how the characters and world react or interact with it, what we learn about the characters because of what the villain does, and how the villain effects the characters on a personal level. Do some of the characters feel sympathy for the villain or their followers? Do they agree with some part of their plan? How do you resolve differing opinions when one PC thinks they should slay all of the villain’s followers but another believes those followers can be saved? What moral lines will the PCs cross in order to defeat the villain?
A lot of villains have offered some kind of encounter or philosophy that have made the PCs reconsider their views or actions, and I think that is a powerful tool.