Ursula K. Le Guin - The Left Hand of Darkness (well, hermaphrodites)
Joe Haldeman - The Forever War
Hero - Perry Moore

The Perks of Being a Wallflower by Stephen Chbosky
Son of a Witch by Gregory Maguire
The Privilege of the Sword by Ellen Kushner and Delia Sherman

Havemercy (fantasy) aaaand a really funny read, The Vesuvius Club.

This is All by Aidan Chambers{Just a warning, it's a long book--but for me at least, it went by fast. It's awhile before the gay character shows up, but I think he's worth the wait. Even though he's a minor character he's my favorite}

Nick and Norah's Infinite Playlist by Rachel Cohn and David Levithan

Lost and Found by Carolyn Parkhurst has a "reformed" (via a church program) gay man and lesbian married couple, and a third gay character. it is a really good book all around, too.

"Naomi and Ely's No-Kiss List" by Rachel Cohn and David Levithan. It involves the girl Naomi's love for her gay best friend Ely, who kisses her boyfriend Bruce. I personally didn't care for the multiple perspectives outside of the main trio - for one chapter, you hear from one girl and ... never hear or see her again after that - but it's a sweet story overall.

My favourite teen lesbian book was Hello, Groin. A classic is Annie on my Mind, though it's not entirely upbeat. Keeping You A Secret, Empress of the World, Kissing Kate, they're all worthwhile, too.

As for regular lesbian fiction, I second Rubyfruit Jungle. And Oranges or Not the Only Fruit (anything Jeanette Winterson does wins). But my favourite author of lesbian fiction is Sarah Waters. They're historical, but I usually hate historical fiction and I ADORED these, so don't write them off. Because of the time period, they don't portray lesbianism as easy, but I wouldn't say it's anti, either. They're long, but read Fingersmith for the crazy amazing plot and to get hooked on her writing, and Tipping the Velvet for the ending, which is my favourite ending for a book of all time. :D Night Watch is also good, but I haven't read Affinity yet. I will soon.

As for the GBT... I don't know. I've heard awesome things about the Rainbow Boys series, but I haven't read it yet.

I'll second the Sarah Waters recommendation. Her books are historical but very good.

I recently read 'Before the Rain Falls' by Jonathan Coe. The narrator of the bulk of the book has been a lesbian and though it is not central to the story she is relating it certainly figures.

"The Steel Remains" by Richard Morgan is a modern fantasy book with two gay main characters.

Have you read My One Night Stand with Cancer by Tania Katan? It's a Memoir, but it's excellent, read likes a novel, and the main character is a lesbian.

My all time favourite is 'The Charioteer' by Mary Renault, which is set during the second world war: also her books about Alexander the Great, though these are a little dryer.

Diana Gabaldon's historical/time travel books (huge, but quick reads) have a minor gay character, Lord John, who steals the show for me. He doesn't turn up in the main series until the third book, 'Voyager', but she also wrote some 'spin-off' mysteries about him, starting with 'Lord John and the Private Matter'.

Others - plenty of gay/bi protagonists in Tanya Huff's books, including the vampire ones starting with Blood Price (I think) and the Quarters books (fantasy).

I loved Alexis and Memoirs of Hadrian by Marguerite Yourcenar.
The first was the first coming out story in literature, it's really heart-breaking and honest, while keeping a style that reminds you of great French classics- it never mentions the word "homosexual".

YA book: Boy Meets Boy by David Levithan. It's not really realistic as the setting is a town where everyone is accepted for who they are. No one blinks an eye. For example; because of the national Boy Scout's policy of no gays, the town simply changed the name of their chapter and life when on.

However, it's fun and sweet, has a good cast of characters, and an nice easy read.

Misfortune by Wesley Stace. It's about
a boy raised as a girl in 19th century
England. It takes a while to get into,
but I thought it was well worth it.

Someone mentioned it already but I just read Hero by Perry Moore and enjoyed it. It is about a boy who has super powers and is gay, two things that his father (a former costumed hero without powers but is now disgraced) seems to disapprove of. It's good.

Anything written by Alex Sanchez (although one you finish reading his main series 'Rainbow Boys' then it's pretty easy to guess the plots of the others)

Blind Fall by Christopher Rice was also very interesting. He does not have the same writing style as his mother, I'll let you know.

This is kind of a stretch, but a lot of John Varley's science fiction stories and novels deal with environments where sex change is easy, painless, and common. There's at least one such story in The Persistence of Vision, and the main character of Steel Beach spends roughly half the book as a man, and half as a woman.

If you haven't read Lynn Flewelling's other series, the Tamir trilogy (Starting with The Bone Doll's Twin, it definitely has stuff involving gender dysphoria and homosexuality.

Sorry if I repeat any of the above. I just skimmed them a bit.

Annie on my Mind - Nancy Garden
The Bermudez Triangle - Maureen Johnson
Swordspoint - Ellen Kushner
Boy Meets Boy - David Levithan
As Meat Loves Salt - Maria McCann
Kissing Kate - Lauren Myracle
Keeping You a Secret - Julie Anne Peters
Rainbow Boys - Alex Sanchez
And anything by Poppy Z. Brite. You might need a strong stomach for her earlier works, though.

Sarah Waters, Fingersmith, Tipping the Velvet, and Affinity. Waters has a strong Dickensian streak (which I love), creates wonderful characters and has incredible story-telling ability. Tipping the Velvet is, in a nutshell, kind of a lesbian Tom Jones. Fingersmith (one of my absolute favorite books of all time) takes elements of Dickens' Oliver Twist and Twain's The Prince and the Pauper and creates an intriguing, unforgettable tale of a girl raised among a den of pickpockets, con men and petty thieves (very similar to Fagin's band of pickpockets in Oliver) who is set up as a lady's maid for a wealthy, innocent young girl in an elaborate con to marry the girl off and steal her money. The plot twists and twists again, and Fingersmith is heavy on the Dickensian characterizations, in a good way (e.g., the baby-mongering den mother to the group of pickpockets, con men and petty thieves is named Mrs. Sucksby). Affinity is the darkest, most depressing of the three, dealing with a women's prison and spirituality (aka, mediums and spirit circles) in Victorian England, again with lesbian undertones.

Emma Donoghue's Slammerkin also mines some of the same subject matter as Sarah Waters' books (young girls overcoming hardships in Victorian England), although I prefer Waters' writing style and story-telling ability. Donoghue's book is based on fact, though, of Mary Saunders, a working class girl in 18th century London who was accused of killing the woman she worked for, Mrs. Jones, a local seamstress, with a cleaver. Donoghue tells the tale of a young girl who longs to get away from her poor seamstress mother and have the finer things in life. When Mary steals a red ribbon from a street vendor, she runs from the law and hides out in Rat's Castle, taken under the wing of prostitute Doll Higgins. Realizing she can't return to her family, Mary allows Doll to teach her the trade, among other things. When Mary eventually falls afoul of a local pimp and con man, she makes her escape to a small town on the outskirts of London where she hides her past as a prostitute and takes up work as a seamstress for Mrs. Jones, a loving family woman who eventually opens her heart to Mary and begins to trust her. Donoghue, a well known English lesbian author, again keeps the lesbian elements as an undertone, but throughout the tale Mary Saunders remains very much her own woman.

One of Sue's first memories in Fingersmith (main character) was of going to see the play "Oliver Twist" with a young pickpocket girl. (This wasn't the musical, of course, which came later in the '60s, but a play taken from Dickens' novel, which was written in the late 1800's.)

I just started re-reading Island in a Sea of Time, by S. M. Stirling, and the military commander of the time-slipped island of Nantucket is a lesbian. Very good books, although some Avonlea/Snidely Whiplash syndrome (Many of the characters are impossibly good or evil).