From comics: Harvey "Two-Face" Dent. Perfect mixture of tragedy and obsessive, villainous mania. The whole "Long Halloween" storyline gave me a huge appreciation for the character. I even have a two-sided suit in my wardrobe.
The Penguin. Love his affectations, his obsessions, his blustery manner of getting things done.
Brainiac 1.0. Have to love an A.I. supervillain, one who can transfer his mind between bodies, and can simultaneously control tiny nanobots and giant, skyscraper-size skull-ships. What absolutely clinched it for me was "Whatever Happened to the Man of Tomorrow", in which Brainiac's head-unit grafted itself onto Lex Luthor and controlled his mind. After a while, Lex managed to splutter out "Kill me", and the request was granted... but minutes later, Brainiac started to force electrical impulses through Luthor's corpse, forcing it to move and continue to host the head-unit. Macabre and fantastic.
From books:
HAL. Absolutely love the character. An onboard computer with a vast intellect and what is possibly the robotic equivalent of a personality disorder? Perfect. In 2010 he's no reprogrammed by his creator and seemingly "rehabilitated", but I'll have to see where the series goes.
Roose Bolton. I despise him for what he's done, but I love the image: nearly pure-white eyes, a voice barely above a whisper, lying on his bed letting leeches "thin" his blood. Creepy as hell. He's the only one on this list that I actually feel hatred towards, though, and the only one I'll be pleased to see perish.