Here Be Dragons by Xela
Summary
Cas accidentally BAMFs himself and Dean into Stargate Command. Hilarity ensues.

http://archiveofourown.org/works/453014


Sex Corps by epeeblade
In a galaxy torn apart by war, there are those agents specially trained in the erotic arts... Or the one where there's a BDSM Planet.
Notes:Also known as the "BDSM Space Opera AU" this all started as a short story I wrote for Lapillus's birthday. 400,000 words later, you can see how well that ended up.
http://archiveofourown.org/series/710

Three Grams by frostian
Summary: Jared Padalecki’s closest friend is Jensen, a hybrid doll he rescued as a child. As they grow up, Jensen takes on the role of tutor and mentor, preparing Jared for the arduous task of entering a prestigious tech in order to continue his father’s tremendous legacy. But the greatest lesson is one that can only be learned, not taught, as Jared realizes that just because a creature isn't made of flesh and blood does not mean it can't have a soul.
http://frostian.livejournal.com/73146.html?mode=reply

and the sequel

Perdix's Lament
Summary: Humanity is at the brink of war as the relationship between the two major ruling parties disintegrate under bloody assassinations and accusations. Representatives from both sides, desperate in the hopes of avoiding annihilation, meet in secret, trying to stave off a conflagration that would set back humanity into the days before space travel. But neither party knows that there's a third group keen to see war explode across all systems. (Conclusion to Three Grams.)
http://frostian.livejournal.com/118304.html?mode=reply

Also, this is an unfinished WIP, but it's just so great I had to include it,

Rule 26 by fleshflutter
A mash-up of Star Wars, Flash Gordon and a few other sci-fi stalwarts.
In which there is a galaxy-spanning evil empire, a mission to kidnap a henchman of the aforementioned evil empire, and Jared is a resistance fighter on the aforementioned kidnapping mission.
http://fleshflutter.livejournal.com/?skip=10&tag=rule%2026

I started an Excel doc listing my sci-fi related fic, with summaries and fic links, after seeing your post about starting the new com. Unfortunately, I haven't had the time to complete it yet. I'm at 114 stories and I'm only about 1/3 of the way through, and I haven't even touched on crossover fic yet. Would you be interested in a copy, if not I'll just keep it for my own convenience.