I've always wanted to make one of those comprehensive rec sites, but hey, I might as well admit it's never going to happen. And so, in no particular order:
Raising Atlantis by Geogirl
Jack-centric, PG-13, complete
What happens when your world collapses?
Uninvited and
RSVP by Ossian
Sydney/Sark, PG-13, complete
All's fair in love... and bio-warfare.
Forty Winks by elise2
Sydney/Sark, NC-17, one-shot
Syd, Sark, and a shot of tequila. Lines are crossed, liberties taken. AU, Syd POV.
Left Turns by Kim
Sydney/Sark, NC-17, one-shot
She thought back on all the choices she made to get to this place, looked for the single obvious detour. The pattern revealed itself only as a series of small turns to the left instead of to the right.
Salt Water Secrets by poisontaster
Nadia/Sark, NC-17, one-shot
All families have their secrets, written in salt water--tears, semen, blood--and visible only when exposed to very strong light. This is hers.
Nothing More to Say by Legalblonde2005
Sydney/Vaughn, PG-13, one-shot
The choices we make when we fall apart.
Magenta by Eretria
Sydney/Sark, R, incomplete
When he talks to her she never responds.
Elysium by Lila2
Sydney/Sark, NC-17, incomplete
Sydney discovers where she's been for the past two years
Scylla and Charybdis by Nes
Sydney/Sark, PG-13, complete
Sydney is caught between a hard place and Sark's ex-girlfriend. Er, not that hard place. Ahem.
Fade by Agent Otter
Sydney/Vaughn, PG-13, one-shot
It's safer that way, to remain constantly on the move. But this isn't the first time that they've sacrificed safety for something else.
Graffiti by darkstar
Sydney/Vaughn, PG-13, complete
Sydney and Vaughn attempt to reconstruct their lives after barely surviving SD-6's discovery of their identities.
Unravel the Mind by Nic-chan
Sydney/Sark, NC-17, incomplete
With Sark lost in a coma, it’s up to Sydney to use a Rambaldi device to save him from himself and from death.
Surveillance by Kantayra
Sydney/Sark, NC-17, complete
Basically, Syd gets stuck doing surveillance on Sark, is not amused, and so entertains herself by staring at his butt. Isn't that a lovely, non-literary summary?
This is Not a Truce by equisetum
Sydney/Sark, NC-17, incomplete
The winner, as ever, is a mystery. But I think it’s clear that both of us are losing.