Nuriko in Fushigi Yuugi - crossdressed for most of his life in honor of his late sister.
Tamahome, Tasuki, and Chichiri also had to crossdress at one point. Wait... and so did Hotohori. Guess all the FY boys have been in dresses...
Meguro from Tokyo Mew Mew a la mode wears a girl's uniform to sneak into an all-girls school.
If we're talking girls.....
Haruka from Sailor Moon wears boys clothes and is often mistaken for a boy. The heroines of Girl Got Game and Hana Kimi also disguise themselves as boys.
I wonder why crossdressing is so popular. ^^;;;; Perhaps because Asians can tend to be more androgynous and can pull it off more easily?? Seeing Western people crossdress usually scares me, but seeing it in, for example, Japanese visual kei bands, I think it looks kinda cool. ^^;; And of course anime characters can get away with it and look absolutely awesome.