I'm not as widely read in YA as some of my author friends, but the following LGBT YA novels are all utter gems. Skip them at your peril! :)
Two Boys Kissing by David Levithan. Okay, this should read anything by David Levithan, because the man is a genius. But this book wrecked me. It has a really gutsy narrative style, taken from the form of the Greek chorus. But the chorus in question is made up of men who died from AIDS during the 80s and 90s. And I knew these men. So while I was reading it I had the uncanny sensation that friends lost were speaking to me. That might be how I managed to cry on every page. Or maybe it's because the writing is just that good.
Simon vs. the Homo Sapiens Agenda by Becky Albertalli. The writing is to die for. This is a pitch perfect story of what it means to be 15 and 16. If you wanted to slap a trope label on the book, it's a coming out story. But it's so much more than that. Ms. Albertalli uses Simon's need to come out as the perfect lens on what it means to be a teenager. Every chapter is priceless. I can't wait for her to write another book.
I'll Give You the Sun by Jandy Nelson. Flawless, amazing writing. This book has about 1000 themes. (Art. Twins. Sexual assault. Death. Divorce. Coming of Age. Betrayal. Family. Ghosts. Addiction. Oh, and somebody is gay.) I'm glad it was never my job to write a synopsis for this book. But READ IT IT'S SO GOOD!
Every Day by David Levithan. This isn't a exactly an LGBT book. But it explores identity of all stripes so beautifully and thoroughly and subtly that it wins a spot on my list. :)
Carry On by Rainbow Rowell. The similarities to Harry Potter are a little distracting. But Ms. Rowell is brilliant, as always. Loved it.