I remember reading this oneshot where one of the characters was a pre-op transsexual. I didn't like it much... but I would like to remember what the name was. Anyone have any idea?

Maybe the oneshot "Ayumi and Aika" in Mermaid Line?

Oh, oops, didn't notice the "yaoi" part >.<

Hrodulf and Bjornolfr, you will not be forgotten.
[img]http://i411.photobucket.com/albums/pp199/SyberAngelGabrielle/couplesig.jpg[/img]
[color=black]And if the world were black and white,
you would be my rainbow in shades of grey.[/color]

Click 'n Play!

If I had a fantasy self, it'd be a tentacle monster.

Nope, as you realized, not that one. I really liked Ayumi and Aika, actually. 😀
Btw, the trans was mtf, not ftm.

Edit: I found it: Mimi-kun no Boy no Kisetsu
I liked it much more than I remembered!