Any where the male lead gets turned into a female via magic or science or whatever. She then either falls for a guy or a girl. So will take straight or yuri ending, but the male lead stays a girl in the end.

Return
Maybe Kanojo ni Naru Hi... though it is more like the second male lead gets turned into female lead in this one.
Edit: (Actually, the Another sidestory might fit better)

~4400 manga completed
~1700 ongoing...

Kakumei no Hi kinda, it's one of my favs. It has a side story that has cross dressing with one of the love interests
Wolf Boy and Cinderella Cute oneshot, pretty open ended though
Return Kind, he dies at the begining but is a girl in the end
Sekainohate de Aimashou A lot of the characters pissed me off, i felt really bad for the main most of the time
Tenshi na Konamaiki very fun, also an anime
Boku to Kanojo no XXX boy and girl switch bodies, the romance isn't between the main boy and girl

The word 'studying' was made up of two words originally - 'students dying'.

Kashimashi - Girl Meets Girl

Boku Girl