Crossdressing

[Kudryavka]

Hayate the Combat Butler's main character cross dresses a lot, but it's done purely for humor, not seriously, so I'm not sure if you'd totally like that. It has both a manga and a few anime series, and the manga is licensed in English by Viz Media.

[Falkor]

there's Hourou Musuko manga (with an anime adaptation already announced). you should definitely check that one out. it deals with gender identity disorder, in which cross dressing is involved.

edit: oh somebody already suggested this one... :P