I'll pull together a quick list of three: Ganon from the Legends of Zelda (I'm going to start calling it Legends, because each game is pretty much its own legend): He is always such an accomplished villain. He usually leads the Gerudo to be a somewhat thriving society, he's perhaps the greatest wizard in the world (I'd wager he's more magically powerful than Zelda, with or without their triforces), he's such a chessmaster with planning, and he's become immortal partly by his own might. He always gets sealed away, but I'm pretty sure he's still never been killed. Handsome Jack from Borderlands: The king of trash-talk and ego, and surprisingly one of the more understandable villains I've encountered. He's a completely mad maniac and high-functioning psychopath, but he also loves his daughter dearly and will do anything to keep her safe, even if it's not the right thing. Omega from Mega Man Zero: Not only was his final boss fight (spoiler, but it's easy to see it coming from the beginning of the game) one of the most intense video-gaming experiences ever, I loved the message that his encounter has for the theme of the game, which I will boil down to: it doesn't matter what you are, it matters who you are.