Let's be honest: while the vast majority of queer folks are comfortable reading about straight characters, a lot of straight folks aren't comfortable reading about queer characters. Consequently, in genres dominated by straight male authors and straight male readers, gay characters simply don't exist. Or, if they do, they are side characters; their relationships fail; their lovers die; their sexuality is a constant source of pain, and they rarely (if ever!) are shown in normal and healthy relationships.
There is some protection in the romance genre, where m/m literature is steadily growing more and more popular. But, unfortunately, not among other genres.
Lynn Flewelling's books are the exception.
She's well known for her award-winning Nightrunner series. The books aren't what I'd call romance -- they're hardcore fantasy, complete with wizards and swords and dragons -- but they do feature loving gay couple as the protagonists.
Let me stress how awesome this is.
Alec -- the main POV character -- is only seventeen when he's dragged off for a crime he didn't commit. In prison he meets Seregil, a charming rogue. Together, they escape and go on the run. Unable to shake a strange interest in his companion, Seregil decides to make Alec his apprentice, and begins corrupting the sweet innocent boy, teaching him arts such as killing and thievery.
Everything about this series is excellent. The worldbuilding, the prose, the pacing, the action, everything. I adore all of it! I'm getting worked up just thinking about it!
A common theme in fantasy novels is the band of heroes; the fighter, the wizard, the tank, the sneak, the girl, ect, ect. Instead of following that trite convention, the Nightrunner series focuses on two rogues, which is enormous fun. Rather than face challenges head-on, they lie, cheat, and steal their way to victory, all in the name of their queen.
The romance, meanwhile, is slow-burning and intense. While there's a huge amount of subtext (and outright teasing) in book one, it's not until book two -- after the two men have been together for more than a year -- that they even notice they're attracted to each other. By then, Seregil likes Alec far too much to risk their friendship for something more. Alec, meanwhile, is confused and uncomfortable with his attraction Seregil.
I'm a huge sucker for this kind of romance: the desperate pining, the unwanted attraction, the almost-too-late realization. The climax is very sweet, and I found myself reading those pages over and over again.
Even long after the two have come together, their relationship endures; they fit together, two very different people that support each other through dark times, even when Alec is being foolish or Seregil is being cruel.
I don't think I have a single negative thing to say about these books. The romance grows much stronger as the series progresses, and it will keep you coming back for more.