Video Games:

Xenogears, by Squaresoft, character Fei/Id. Fei is the tortured hero, but he ends up integrating, and Id is a big ol' villain for the duration of the game.

Final Fantasy 7, by Square, character Cloud. Now, he's not really multiple, but he's just kinda muddled in the head with symptoms thereof....Good enuf, until we get something else.

Planet Laika: ?