Hmm, Not normally the stuff I watch. I prefer love triangle comedies. I suppose in that vein all toss out
Kashimashi: Girl meets Girl , The Hazumu & Yasuna pairing as one of my favorite yuri couples. I like
Maria-sama ga Miteru, but can't say I have a favorite pairing in this show.
I also enjoy
VanDread and
Saber Marionette J, although neither really has a pronounced yuri or yaoi pairing, there is plenty of effort being put in by Mitsurugi Hanagata in SM-J to be with Otaru Mamiya, probably one of my favorite humor based unrequited yaoi pairings. Since both shows are supposedly based on societies that are all men or all women, it is surprising that there isn't more obvious yaoi or yuri pairings.
Simoun, a show that came out two years ago will provide plenty of yuri for those who like it. It is about a society composed entirely of women that are given the choice to change gender when they turn 17. If that isn't weird enough they fly around in mechs that can only be operated by the young women who haven't made a choice yet. Can you say lesbian angst? Plenty of it here.
If you like yaoi/okama characters, you might enjoy Hana from
Tokyo Godfathers or Ginka Midarezaki from
Kyouran Kazoku Nikki, I love that show. Each character has their own ending theme.
Here is Ginka's.
I have seen other shows with hinted unrequited yuri relationships, but I think these are all of my favorites.