Nobody mentioned Ergo Proxy yet?
It's a series about a people who's job is to hunt down robots that have got religion / gone bugfuck crazy.
Gorgeous animation, but the series suffers slightly from Eva syndrome (director apparently going batshit insane towards the end). That being said, at least it has pretty clever mindfuckery, and the whole thing is very high quality. The characters are engaging and well written, and Pino, the little girl robot, is both cute and creepy.