*Flame shield up*
The Joker. Seriously, it's fine if a villain clowns around and does stupid s***, but we're supposed to believe that he's also a super-intelligent mastermind, has good fighting skills (Arkham Asylum, anyone?), and continually escapes prison and gains a legion of followers? Not only that, but he steals the spotlight from Batman, is completely cocky, and everyone seems to love him, fans and all. F*** that, I say. He can go choke on roped turd.
Other runner-ups: Rogue the Bat, the kids from Twilight Princess, Atlus from Bioshock (flame shield stil up), Ratchet (at times), several characters from Lost and 24, the old lady from Be Kind Rewind (god I wanted to kill her), Farah (feminist to the extreme) and possibly Chloe from Uncharted. Phew, I think I'm done.