i wanted to bump this because i've been thinking a lot about it, and because a rewatching of grave of the fireflies & the filmspotting discussion of waltz with bashir prompted me to develop a stance on this.
as far as the use of animation, and how it can be used OUTSIDE of fantasy or fantastic settings to good effect, in both grave & bashir it's utilized in such a way as to place a layer of abstraction between the audience and the horror of the events that are taking place. in this way, people to whom the material would be otherwise inaccessible is now accessible.
further--and i should state that i haven't seen the film, and i therefore can't speak to this personally--according to the filmspotting guys, bashir uses a shift from animation to real footage to great emotional effect.
i would also add waking life to the list of films that use animation in a unique way, there utilizing it to convey the dream-like state of everything that happens in the film. it does not detract or make the film lesser in any way, and if the events there were portrayed with plain, real footage, that dreamy ambience would be lost.