Yeah, yeah yeah. I know, horrible stereotypes, but as far as a gender-bending comedy that actually handled things somewhat sensitively and didn't use the gender bending itself as a massive "ZOMG MAN IN DRESS" joke?
Mrs. Doubtfire.
Yes, Robin Williams messed around and made some off-colour jokes regarding swapping gender roles in the movie, but when Robin Williams was Mrs. Doubtfire, he was generally acting the part of a woman, albeit one who was inept in certain areas, rather than acting the part of "Dude in dress."
Y'know?