Lane Robin's Maledicte contains crossdressing that flirts around the boundaries of the trans* spectrum, and as a result some apparently homosexual relationships. It's one of my favorite books—the way it blurs the lines of "normal" gender and sexuality doesn't strictly fall into this category, but it's all certainly queer.
Gilbert Adair's The Dreamers (a.k.a. The Holy Innocents) has a m/m/f threesome, and therefore a gay relationship. It's also a fantastic book.
Michael Cunningham's A Home at the End of the World has two protagonists, one of which is a gay man, the other of which has gay relationships. Also a fantastic book.
Exquisite Corpse should be added to Poppy Z. Brite's list.
Ignoring the subtext in the first three books, The Tale of the Body Thief from Anne Rice's Vampire Chronicles has an explicit homosexual relationship between Lestat and David Tabolt.
Frank Wedekind's Spring's Awakening (a.k.a. Spring Awakening) (a play) has a homosexual relationship.
Donna Tartt's The Secret History has a gay character in the core cast, and some homosexual relations. Fantastic book.
Tana French's The Likeness has a single homosexual encounter—it's not quite incidental, but also may not qualify the text for this list. Fantastic book.
Kathe Koja's Under the Poppy has a homosexual relationship at its heart.
Many of Caitlin R. Kiernan's short fiction contains queer content—The Ammonite Violin & Others is a particularly strong example (and fine collection).
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Gilbert Adair's The Dreamers (a.k.a. The Holy Innocents) has a m/m/f threesome, and therefore a gay relationship. It's also a fantastic book.
Michael Cunningham's A Home at the End of the World has two protagonists, one of which is a gay man, the other of which has gay relationships. Also a fantastic book.
Exquisite Corpse should be added to Poppy Z. Brite's list.
Ignoring the subtext in the first three books, The Tale of the Body Thief from Anne Rice's Vampire Chronicles has an explicit homosexual relationship between Lestat and David Tabolt.
Pauline Réage's The Story of O has some bisexual content, and one of the central female/female relationships is partially sexual. Another fantastic book.
Frank Wedekind's Spring's Awakening (a.k.a. Spring Awakening) (a play) has a homosexual relationship.
Donna Tartt's The Secret History has a gay character in the core cast, and some homosexual relations. Fantastic book.
Tana French's The Likeness has a single homosexual encounter—it's not quite incidental, but also may not qualify the text for this list. Fantastic book.
Kathe Koja's Under the Poppy has a homosexual relationship at its heart.
Many of Caitlin R. Kiernan's short fiction contains queer content—The Ammonite Violin & Others is a particularly strong example (and fine collection).