I absolutely love Takako Shimura's "Hourou Musuko" is by far one of my favourite stories as the main character is transgendered and struggling with it. I figure just about anyone here would either identify with Shuu or tatsuki. 10 volumes in and I still can't get enough.
The same mangaka does "aoi hana" and that is another decent one. Then again I love yuri, I also like Sasameki koto, I think it may be a bit better than Aoi Hana. Girlfriends and Ameiro Kouchakan Kandan are also among my favourite mangas, all of which are in the yuri genre.
Legends of Galactic Heros, Elfen Lied, Bleach, and obviously Strawberry Panic! are also all great series that I like alot, even though I probably prefer the anime of these ones (even though the anime of elfen lied was really short).
Oh, and Azumanga Daioh always makes me smile, even on the worst of days