Rain "Rain" is a comedy/drama that follows the daily life of teenage transsexual (who is coincidentally named Rain) attempting to go through her senior year being only identified as a woman.
Yellow Brick Ramble A reboot of The Marvelous Land of Oz (the sequel to The Wizard of Oz) reimagined as a trans coming out story and also as a romantic comedy road trip.
I want to be a cute anime girl Charon's sister dressed him up as a girl, and he liked it. This is their story, learning about who they are, and their friends and family around them.
Clover & Cutlass Do you wish there were more shoujo manga about orc girls kissing?
Court of Roses Follow a ragtag group of bards as they band together and travel the realm of Prismal
Do Webcomics count?
If so:
I'll add more if I remember more of them