Haven't you guys seen Mulan? Then again, that was more about breaking the mold in terms of gender roles than dealing with gender identity.
Wandering Son - Wikipedia, the free encyclopedia
I hadn't read the manga, but the I liked the animated adaption of "Wondering Son". It pretty much revolves around two kids in 5th grade, one (a girl) wanting to be a boy, and another (a boy) who wants to be a girl. Imagine going through puberty with all of this happening, not sure about who you are, or better yet, not knowing what to do. It's full of pretty awkward moments, most of them from the male protagonist in the story.