Here is my collection of yaoi fiction. It's mostly Roy/Hughes and it's rather small, but I imagine that it will grow in time.
Roy/Hughes
A Kiss For the New Year: Hughes drags Roy out to celebrate the New Year. PG-13, no spoilers.A Matter of Chance: Maes Hughes has never been afraid of risks, and he isn't one to let a little thing like gender stop him now. R, no spoilers.
The Still Point of Destruction: Roy is a broken man. Maes Hughes is willing to do whatever he can to fix him. R, spoilers for episode 13 - 25.
A Drunkard's Prayer: Even as things changed, they always remained the same. PG-13, episode 25 spoilers.
Misc
The Hunter Takes His Prey: Face to face and without any backup, Roy faces Scar. NC-17, Scar/Roy, 13 - 25 spoilers.
I Would Be You: Envy never gets the things he really wants, but he's learned how to fake it. Envy/Envy, Envy/Ed, NC-17, full series spoilers.