I can blame this fandom on Ciceqi, as well. She turned to writing FMA after her stint with Saiyuki (or maybe that's reversed) and I followed. :D Only the 2003 anime, with manga!Ling as a fun addition; I can't keep track of the manga, and some of what goes on there seems a little too cracktastic even for me. Plus, I like the idea of the Alterworld.
EDIT: 8/15/16; I started reading a couple of new epic length fics and rekindled my interest. There's some more manga and 2nd anime based fics mixed in now.
~Harukami. Start at her website, and then check out her journal for newer stuff.
~The Touka Koukan Archive has a ton of fic, for just about everything and everyone.
One-shot or Short Fics:
~An Interesting Trip, by Shanastoryteller. AU, with the first words that your soulmate tells you written on your body, it's a trick to keep yours from figuring you out. Ed/Roy, Hawkeye/Havok, Maes/Gracia, Al/Winry. Bonus points for both uses of the title phrase.
~Build your wings on the way down, by Shanastoryteller. Ed learns a hell of a lot more from the Gate, and this naturally affects his plans and opinions of people in the military. A half-complete WIP, but definite hints of Ed/Roy.
~Cause for Concern, by Metisket. Havok's first time driving the Elrics. Gen.
~Girls Who Wear Glasses, by Mikkeneko. Of course Ed would think an eidetic memory was a turn-on, especially during sex. Ed/Sciezska.
~Ignis Fatuus, by Mikkeneko. Ed redirects his life, post-Al's recovery, towards deconstructing human chimeras. Gen.
~Weddings, Xing Style, by Youkofujima. A cute set of drabbles about culture shock during a wedding. Ed/Mei.
~A terrifying clamour of trumpets, by Shanastoryteller. Ed is coming down with the same terminal illness as his mother, and keeps it a secret from most of those whom he loves while stepping up the pace on his quest. A small nod to the anime series at the end, specifically the alterworld. Ed/Roy, eventually.
~The Adventures of Roy Mustang, Sex Ed Teacher, and sequel Better Living Through Alchemy, by Skydark. The first covers an awkward romance during the series canon, Roy's devastation during Ed's presumed death/stay in our universe, and a non-canon return and reconciliation. The sequel covers Ed as an Alchemy teacher for military kids. Ed/Roy.
~The Alter series, created by Hime1999. Illustrated fics, covering a different alterworld timeline - like if, say, Alter!Roy showed up as a young Japanese research assistant. Gen, but very strong UST for combinations of Roy, Ed, and alter!Roy, and even Van Hohenheim is someone's crush.
~Come What May, by Batsutousai. The first part of a WIP series, this one diverts from the manga climax, with the change being that Ed doesn't give up his alchemy; consequently he stays in the military and gets a posse (a mix of chimera and new officer recruits) as he tries to prevent terrorism in the new Amestris. Planned to be Ed/Roy in sequels, currently Ed/the chimeras Heinkel and Darius.
~Dark Humor, by Jellymeat. An Ed/Envy mpreg - don't run! It's angsty, with death hanging over their heads the whole time, and some good action at the end. It certainly isn't a sappy romance, and that's why it's good.
~The Familiar series. A sweet illustrated-fic series about Ed and his son by an unknown OC. The illustrations are as good as the sappiness. Gen.
~Full Circle, by Nike Femme. Ed went to a different Verse post-series, and the Ed that came back is a whole new person, who doesn't remember his life pre-Gate. Ed/Roy.
~Ishvalan AU series, by Shanastoryteller. If Trisha had been Ishvalan, which parts of the story would change, really? I liked her character in this; even though she's still a posthumous character there's plenty of flashbacks from her POV. The Ishvalan culture was also refreshing. Trisha/Von Hohenheim, Ed/Roy, implied future Winry/Scar.
~Reverti Ad Praeteritum, by Batsutousai. Ed goes back in time to his first view of the Gate, in an accident that occurs long after he's been married to Winry with kids; while he misses the kids, he takes the opportunity to fix problems before they start - and those problems range from "Father's apocalyptic plan" to "my unhappy marriage". Lots of fun explorations of tangential manga topics and snowballing changes to plot (ex. Al and Ed spend a few years in Xing studying alkahestry). Endgame of Ed/Roy.
~Fading Footsteps, and sidestory, by Stickmarionette. A crossover with Harry Potter, done intelligently. Of course Ed would be around in the early 20th century, in this Alterverse... so the student he would meet and influence would be Riddle. Immortality, putting souls in objects - it all fits now.
~Field Maneuvers, by Aster. A fusion with Final Fantasy 7; Sephiroth meets Greed the SOLDIER, and his team. Later fic are purely about Greed's team, and new members. Greed/everyone at some point.