9. Clayface - Batman: Arkham City
In one of the most ingenious gaming bait-and-switches of the last decade, Batman: Arkham City reveals near its climax that the healthier Joker we've been interacting with for most of the game isn't actually the Clown Prince of Crime at all.
Rather, a very, very sick Joker - who is suffering from blood poisoning due to ingesting the Titan formula in the previous game, Arkham Asylum - has enlisted shapeshifting villain Clayface to assume his identity and pose as a less-sick version of himself.
It comes as quite the surprise to even the Dark Knight, and when the real Joker finally emerges he even gloats about the fact that he hid Clayface right in front of Batman, telling him, "So, how do you keep a secret from the world's greatest detective? Well, do you know? You stick it right in front of him, right under his long, pointy nose... and wait!"
Inquisitive players are able to figure out the twist early, however, by scanning the imposter in Detective Mode, where they'll see that he doesn't have a skeleton and therefore cannot be the real Joker.