the only example i know is no bra

Kiss Me Princess should fit perfectly.
Ame Nochi Hare (BIKKE) might work, but I haven't read it.

You could also try the gender bender + shounen-ai genre search.

That happens in Mint na Bokura and Tenshi Ja Nai!!. My Barbaric Girlfriend and Click could sort of count...kinda.

Kunisaki Izumo no Jijou--the dude who is crossdressing is straight and doesn't hold any feelings for the dude thatz crushing on him

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Angel Beats--best anime of the 2010 spring season

there is an accidental situation in +C: Sword and Cornett

Mizuho Ambivalent
His/her senpai knows, but doesn't give a rats ass and annoyingly/obsessively pursues anyways.

Return

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Happens in zippy ziggy.

Mangetsu Monogatari.

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Prunus Girl
But it's weird, like everybody is okay with a shemale in highschool, no reaction about it... But you never know if that's a male or a woman, or what..