The ones with gay/lesbian characters are, to the best of my recollection:

The Heritage of Hastur (POV male character)
Hawkmistress! (Significant supporting male character)
The Renunciate arc: The Shattered Chain, Thendara House, and City of Sorcery (POV female character and several significant supporting characters)
The World Wreckers (POV male character ends up in a relationship with a hermaphrodite who he initially perceived as male)

I'm pretty sure the Renunciate novels and The World Wreckers must have been marketed as adult. . . there's some moderately explicit sex, for one, and all the characters are adult. The Heritage of Hastur and Hawkmistress! could have been marketed as YA. . . they feature teenage protagonists, at least, and aren't explicit. . . but given that the rest of the series is aimed at adults I couldn't say for sure that these were marketed differently.