Brief descriptions in list format...
.hack//sign: Japan, series 2002. Unique in that this anime takes place almost entirely within a Massive Multiplayer Online Game in which Tsukasa is mysteriously trapped, unable to log out. He meets and befriends a wide variety of other players who team up to try and solve Tsukasa's problem, which only uncovers a much larger plot within the system. Specifying the yuri content here spoils the suprise.
"Kannazuki no Miko": Japan, 2004 series. In short: two girls (Chikane and Himeko), best friends, turn out to be the reincarnated Lunar and Solar priestesses who must battle the evil 8 Orochi to restore the world to balance. Chikane is in love with Himeko, who herself is torn between male childhood friend Oogami and her best friend Chikane.
Kasimasi: Japan, 2006 series. A boy, Hazumu, is hit by a stray alien ship and killed. The aliens, in apology, make a new body for him - unfortunately, he is now irreversably a girl. Hazumu has two best friends who are girls. One was falling for him when he was a boy but now struggles with her feelings now that Hazumu is a girl. The other girl Hazumu fell in love with as a boy but was rejected by her - but now that Hazumu is a girl, she wants him/her. Everyone around Hazumu has to adapt to Hazumu now being female - and oddly, Hazumu is the one person LEAST bothered by it. Lots of gender issues are brought up without being actually talked about. And there's a happy lesbian ending. :D
Maria-Sama ga Miteru: (Japan 2003-04) Anime series. One main character is DEFINETLY gay, and you can argue that most of the rest of the nearly all-girl cast is as well. TONS of subtext and maintext. This series has little in the way of plot as most people know it; it's all about character development, and this series has by FAR the best character development of any show I've ever seen. About a group of girls who attend a prestegious all-girls Christian school where elder students take on "petite soeurs" (underclassmen) and guide them through their lives while attending Lilian.
Noir: Japan, series 2001. Film noir style anime about two female assasins who have mysteriously linked pasts that are coming back to haunt them. The yuri content of this series isn't obvious - though it was way more obvious the second time I watched it.
Puni Puni Poemi - Japan, anime, subtitled. IMDB says: "This is a 2-part OAV spin off of the Japanese anime series "Excel Saga". Shinichi Watanabe returns to deliver some of the most outrageous, outlandish, series that parodies the magic girl anime (ie: Sailor Moon). However, this thing has a lot of perverted humor including 10-year old lesbians, incest, and lots more. You have been warned!". Yes. This is just one huge parody of all anime, and the lead character is a lesbian. It's not reeeely perverted at all, but you have to have a good and slightly off-beat sense of humour for it. I just HAD to put this on the list.
Revolutionary Girl Utena - Japan, anime (series 1997, film 1999). The mother of all current yuri anime. Also very bizarre, stylistic, symbolic, and difficult to watch, unfortunately. The film has nothing to do with the series, just reuses characters and motifs. Both feature tomboyish Utena, new to Ohtori Academy, who is thrust into a strange and dark world of sword dueling for the ultimate prize: Anthy, the Rose Bride, and the key to Eternity. In either version, Utena duels at first because she's dragged into it and second to protect Anthy's honor as a human being while everyone around her treats Anthy like a piece of meat. Both result in mutual respect and desire, though the point of the series is far more abstract than that.
Simoun: Japan, series, 2006. In short, this entire series is voiced by a female cast, even male characters. Everyone on this world is born female and at age 16 or so can choose their future permanent gender. The country of the main characters is in posession of strange, ancient technology that makes them the envy of the rest of the world and thus at war. The technology that drives their fighting aircraft, the Simoun, seems to require a spiritual element: it can only be flown by pre-gender-chosen girls. Before each flight, the girls must kiss the orb that powers the Simoun and before that, they ritualistically kiss one another. Tons of lesbian drama that somehow doesn't seem fanservicey at all.
Strawberry Panic: Japan, series, 2006. Awful, stereotypically, cheezy, whiney, schoolgirl drama-cutsey anime where EVERYONE is a frikkin' clueless lesbian or lesbian predator. Lots of inferred lesbian sex and lots of girl/girl relationships, although as far as kissing goes, nothing has the sheer volume of Simoun, on principle. Not a very deep series, though - it's a wannabe parody of Maria-Sama ga Miteru. Taken as a silly anime, Strawberry Panic is almost enjoyable.
Yami to Bōshi to Hon no Tabibito Japan, series, 200?. Psychotic. Hazuki and Hasumi are (adopted) sisters. On the eve of her 16th birthday, Hasumi disappears - turns out she is actually the demi-goddess Eve. Hazuki is in love with her sister and will stop at nothing to find her as she follows after a random trail of clues through dozens of bizarre worlds contained within books in the Library of Eternity or some such. Highly bizarre and difficult to watch, though not as difficult as ...Utena.