Batman: The Animated Series is actually really well done. I'm a fan of both that and the Christopher Nolan films.
If you like Superman or Batman there are some great animated films out there.
Superman Doomsday is a truncated version of the "Death of Superman" comic saga. After reading that, then seeing the movie, I felt they did it justice. Lots of angst, lots of Lois. I really enjoyed this.
Justice League: The New Frontier is pretty neat; its animation is old-school, even though the movie is recent. Superman shares his screen time with the other superheroes, but if you like action, it's great.
There are two others that I know of: Superman/Batman: Apocalypse (featuring Supergirl) and Superman/Batman: Public Enemies. The first was kind of cheesy, the second I haven't seen.
