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I don't know if he's been mentioned already, but Michael Gambon's character in The Cook, the Thief, His Wife and Her Lover deserves a place on here. Peter Greenaway set out to create a character who could double as an index of the most unkind, ugly and disgusting traits a man could have. He's like an adult character from a Roald Dahl story, only worse.
In terms of charmingly despicable antagonists, Claire Quilty is one of Vladimir Nabokov's best creations, and Kubrick/Sellers turned him into a great movie villain as well. There's a corresponding character in Sean Penn's film, The Pledge. I don't want to give anything away, but the effect it has is creating an unsettling atmosphere, and it's a fantastic example of storytelling, if not a great specific villain you can put a face to (like Anthony Hopkins in Silence of the Lambs).