I Should Have Known by The Medicated Sheep
Sam finds out.

Colony Atlantis by Icarus
m/m sex
Uuuh.. it's kinda a crossover with Atlantis, but I think it's close enough to count. Jack & Daniel move to Atlantis when General Hammond finds out about them.

Walk on Water by dirty diana
m/m sex
Cameron watches Daniel, who isn't quite so clueless.

Jericho by dirty diana
m/m sex, m/f sex, AU
They're bank robbers. And.. uuh. They rob a bank and have a relationship. :D It's good!

Kissing Frogs by Pepe
m/m sex
Lets-get-them-together-fic. XD Romancy and good.

Right Here Waiting by Pepe
m/m sex, non-con, torture
Jack/Daniel, Jack/Sam
Aliens-made-them-do-it fic. :D But with a Ba'al-y twist!

The Gift by Canadagal
m/m sex
Couldn't get through this... x_x Seemed off. Mpreg!Daniel strikes again.

A Second Helping by Seanchaidh
m/m sex, BDSM
Jack's not as young as he used to be. Um. Bondage!Dildo fic. xD;

Mother Of All Dilemmas by Dreuganlady
LONG, m/m sex, non-con, mpreg, kidnapping
Jack/Daniel, Others/Daniel
Not your usual mpreg-- in which aliens conduct brutal experiments on one Doctor Jackson, and the consequences.

Truck Stop by Imagine
long, m/m sex, AU
Trucker!Jack meets huntedbyarcheologists!Daniel. xD It's just... I don't even know. Fun read.

Masquerade by Imagine
long, m/m sex
Daniel gets a shot at going undercover this time.

Coda by Kres
I seriously do NOT remember. It's about that ep where they do that freaky timeline thing... >_> I cannot for the life of me remember what happens in it, though.

Stalker Pete and the General by Mitch H
m/m sex
Jack/Daniel, Pete/Sam
Jack doesn't approve of stalkers-- so Pete has to win him over.

Jack's Viking Sky by Mitch H
LONG, plot, m/m sex, non-con, slavery, kink, kidnapping
Jack/Daniel, Others/Daniel
Jack and Daniel crash land on an alien planet-- Jack seriously injured and Daniel viewed as a religious prostitute. I am in LOVE with this fic. >_> Go read. Like, now.

The Other Side of Me by Mitch H
m/m sex
mirror!Daniel comes through, and shows Jack what life could be like.

The Piano by Mitch H
m/m sex, non-con, kidnapping
Jack/Daniel, Other/Daniel
Daniel used to play the piano-- and there's a very good reason he doesn't anymore.

Unas Means Never Having to Say You're Sorry by Mitch H
m/m sex, non-con, kink
Chaka/Daniel, mild Jack/Daniel, Unas/Daniel
Chaka stakes his claim.

A Mad Wind
long, m/m sex, non-con, kidnapping, slavery, violence
Jack/Daniel, Others/Daniel
While Jack is gone during "100 Days", someone takes advantage.

Tormenter by Clarity
m/m sex, non-con, violence, kidnapping
AU!Jack&Daniel show up through the mirror, with Jack as super!crazykiller.

Waking Nightmare by Elizabeth Lea
long, m/m sex, m/f sex, non-con, violence, kidnapping
Jack/Daniel, Others/Daniel
Some know that there are better ways to break a team than death.

Beloved by Bren Antrim
m/m sex, non-con, kidnapping
Daniel is kidnapped... by male!Hathor.

Shield by Bren Antrim
m/m sex, non-con
Apophis abducts Daniel; Dan

The Annule Series by D. Kelley

Posession/ 2/ 3/ 4/ 5/ 6/ 7/ 8/ 9/ 10/ by CK
Jack gets taken by a host.... but the Goa'uld isn't quite what you would expect.

Jack Daniels Straight Up by Crossbow
Three ways in which Jack & Daniel get together, no frills. I love this for the third one, where Daniel explains away all his straight-ness in the series. XD

Honey, I Shrunk the Physicist by Terry
.....Sam has to be shrunk and sent inside Jack to deactivate the .. mechanism.. in his abdomen. That makes him look like he's pregnant. It's weird crack fic o' humour. xD;

Covert Operations by Mitch H
Just what is Daniel doing while Jack's on the phone?

A Southpark Foothold From Marklar by Mitch H
Spoof on the South Park episode, where all the aliens can say is "Marklar". xD;;