People already mentioned most of the stuff I'd recommend, but I'd second Othello, Dandelion Among Lilies, and Aqua Blue Cinema. Lonely Wolf, Lonely Sheep is pretty good too.
I'm surprised nobody's mentioned Aoi Hana/Sweet Blue Flowers. I don't particularly like it but I thought it was at least as popular as Sasameki Koto, Octave, Girl Friends, etc. It's licensed though so Dynasty doesn't host it.
Somewhat outside the question... Do you mind anthologies? A Knife Edge Girl and I'll Send Her Home on the Last Train are both pretty strong; Knife Edge Girl is two long stories +short continuations and a standalone story, Last Train has two connected chapters but is mostly standalones. A lot of anthologies have similar pagecounts to 1-volume series, but if you're looking for series for longer development of a relationship anthologies probably aren't a great fit.
Yuri Kuma Arashi has a completed anime, the manga is in scanlator limbo. I could say a lot on why it's good and why it's bad but it's already kind of outside the thread's scope so... it's at least worth a try. It's at least as overtly yuri as any manga mentioned so far though, you don't have to worry on that count.