Reddit mentions of Orlando (Annotated): A Biography

Most of these recommendations are sort of peripherally queer, so they may not be exactly what you're looking for, but I figured I'd throw them out there in case you're interested.

I admit I'm not a big fan of it, but Virginia Woolf's Orlando is definitely a queer text. The titular character changes from male to female, and the book itself is often read as a love letter to Vita Sackville-West, the woman with whom Woolf had a love affair. I had trouble getting engaged in it myself, but your mileage may vary.

Santa Olivia (and the sequel, Saints Astray) by Jacqueline Carey features a lesbian romance. Not super heavy, but they're fairly quick, fun reads. Carey's Kushiel series (beginning with Kushiel's Dart) might qualify as queer, in that it embraces and celebrates all types of relationships and sexualities (they are set in a society where the gods' most sacred precept is "Love as thou wilt," and bisexuality and open relationships are typical). The primary love stories are heterosexual, but the characters also often engage in same-sex relationships (both sexually and emotionally), and there are supporting characters of various sexual persuasions.

The Tamir Trilogy by Lynn Flewelling is about the rightful heir to the throne in a troubled kingdom. Born female, she was magically disguised as a boy in order to protect her (the usurper king has been making noblewomen disappear in order to protect the succession of his own son). It maybe doesn't explore the consequences of Tobin/Tamir being essentially transgendered as deeply as it could, but it's an interesting and enjoyable read.

The Left Hand of Darkness by Ursula K. Le Guin is a sci-fi classic that plays with gender and sexuality. The basic concept is that, on the planet of Winter, everyone is hermaphroditic. Le Guin's thoughtful exploration of this world was incredibly groundbreaking at the time it was written, and it remains a really enjoyable and thought-provoking read.

Octavia Butler's work also often embraces feminist and queer themes, playing with sexuality and gender. Fledgling and the Xenogenesis Trilogy are some you might find interesting.

The Female Man by Joanna Russ is an explicitly feminist book with some queer themes. It follows women from four alternate realities (one of which is a utopia populated entirely by women) as they cross over into each others' worlds. It's not always an easy read--it can be very fragmetary--but it's totally worth it.

I also just stumbled across this self-proclaimed Gay Fiction Booklist That Doesn't Suck. Some of the above books are listed, and there are a bunch more sci-fi/fantasy titles that might be of interest.

Happy reading!