Caveat 1: This list is incomplete by any standards. It's based on what I've read, what stuck in my head, and what I've currently got in my tiny temporary space. It does not include Adult books or picture books.
Caveat 2: These books may be flawed. Most books are. There was a time when you couldn't write a book about a gay or lesbian character (never mind the other shadings) without someone dying. We're mostly past that (see one book noted below), but we're getting there.
Caveat 3: Most YA novels (not all) focus on the relationship rather than the sex, but this is not always the case. I have not attempted to mark for explicitness, as it's not something that sticks in my head when I read a novel.
Caveat 4: This list contains no graphic novels. Mostly because my brain is being flaky and refusing to bring any to mind.
Caveat 5: I have read many but not all of these. Some because they went into storage before I had a chance, some because they're on order and haven't arrived and some because I haven't had time. The point of the list is quantitative rather than qualitative.
Note: In some cases, I've noted authors, in some specific titles. If I list an author it is because most of their work contains queer themes.
If there is interest, I can also do a YA books with multicultural themes list.
Chris Crutcher Angry Management Spoiler: the black gay character dies. I was disappointed because up till that point, I'd loved the character. He also has gay characters in some of his other books.
Nick Burd Vast Fields of Ordinary
Brian Sloan Tale of Two Summers
James Howe Totally Joe
Shyam Selvadurai Swimming in the Monsoon Sea
M. E. Kerr
Julie Anne Peters
Malinda Lo Ash
Sara Ryan Emperess of the World
Lauren Myracle Kissing Kate
Maureen Johnson The Bermudez Triangle
Mixed and/or I don't remember
Ellen Wittlinger Hard Love
David Levithan Boy Meets Boy
Garret Freyman-Weyr My Heartbeat
Paul Ruditis Drama! series
Steve Kruger My Most Excellent Year
Adam Rapp Punkzilla
Jacqueline Woodson From the Notebooks of Melanin Sun
James St. James Freak Show
Francesca Lia Block
Lisa Papademetreou M or F?
Ron Koertge Boy Girl Boy
Julie Anne Peters Luna
Ellen Wittlinger Parrotfish
Alison Goodman Eon: Dragoneye Reborn
Meagan Brothers Debbie Harry Sings in French
Lauren McLaughlin Cycler and (Re)Cycler
Nancy Garden, ed. Hear Us Out!: Lesbian And Gay Stories Of Struggle, Progress, And Hope, 1950 To The Present
Marian Dane Bauer, ed. Am I Blue: Coming out of the Silence
Michael Cart How Beautiful the Ordinary