I lean towards Sam/Jack and Daniel/Vala, but there are just as many team fics and action adventure epics.
The be-all and end-all of Stargate archives. There's so much here I can't tell you where to start anymore, so just dive in. Also try Heliopolis 2 for adult fic.
The Stargate Novel Archive
Not going anywhere for a while? Then settle down here and start working your way through the long stories. Start with ELG (The Wine of Dionysus and The Quality of Mercy), but be warned -- they may spoil you for anything else. Anything written by Gracie (The Hidden One), Toulouse (Dancing on the Volcano), Ellen Caldera (Flashback and others), OzKaren (Medical Considerations), DustDevil or Noda (Contagion) will also be worth your time (some S/J shippiness, but uniformly well-done).
A much smaller archive than Heliopolis, but with a much lower signal-to-noise ratio and extremely light on the 'shipper fic. Some repetition of content from Heliopolis, but not a lot, and nicely labelled for content. Look for Brenda Anders (Vindication, Decoration Day, Sense of Touch, Points in Time), Jb and Yum@
Sally Reeve's Fanfiction
Lots of Sam/Jack angst, but solidly plotted, gorgeously written and with dead-on characterization. The Line series rocks my world; A Deadly Legacy and Night Terrors, cowritten with Marcy, are also exceptional.
The Sam/Jack Directory
Good S/J fanfic is hard to come by, but this is the place to start looking.
The lies we tell
suzvoy is S/J to the extreme, mostly short stories written with humor and insight. Good stuff and lots of it.
Denise does it all and does it in bulk -- humor, S/J, S/D, action and character studies. A Presidential Visit and Centre of Attention are both good crossovers, Watch Where You Step and What Is It This Time? are hilarious, Games People Play is a great drama for an unlikely team of characters... Oh, just go read everything. If you have time, cause brother, there's a lot of it.
The Blue Jell-O Metaphor by Jennghis Khan
A funny, slightly poignant Sam character study, who is a little too good at everything except her life. Some really excellent team interaction, and a few nice insights into Super!Sam.
Detour by Penknife
"Vala's very good at slowing them down." A great little Cam and Vala piece (with bonus Annoyed!Daniel).
Folsom Prison Blues by Eve11
"They're all tens if we can get out of them." Another day, another prison; SG-1 never has it easy.
The Furling's Gift by amperage and livengoo
Think Daniel is a lot of trouble as an adult? Try him when he's seven. amperage and livengoo take the old kidfic cliche and make it into something by turns hilarious and touching. Daniel is a little wretch, Jack is coping, and somehow, they both might get through Daniel's second childhood alive. Occasionally on the schmoopy side, but the times when you double over laughing make up for that in big, big ways. Plus, there's this really fabulous crossover.... KikiRec
Honor Amongst Thieves by Cleo the Muse
I love this story. I want to hug it and snuggle it and feed it cookies. A more than novel-length AU of a Daniel Jackson who wasn't returned from Ascension to SG-1, but was instead found on a world in the middle of nowhere, where he meets up with one Vala Mal Doran. Plotty and funny and romantic and awesome -- Daniel the Pirate is almost as cool as the author thinks he is, his partnership with Vala is great fun, and there's lots of SG-1 in the background (including Jonas!). Daniel/Vala all the way.
Magnificent Desolation by abyssinia4077
I have loved the stars too fondly to be fearful of the night. Sam and Jack and NASA and the stars and just completely lovely. Gen.
A Maneuvering Business by daisycm83
A long Sam/Jack fic as written by... Jane Austen? Yes, my children, you read that one right. Crackfic at its finest, the SGC characters taken to Austen's times, and written exactly as they would be then. Familiar faces romp through in unfamiliar roles, but everyone is recognizable and having a wonderful time (except Sam and Jack, but that's only because it's a romance novel -- they have to be unhappy at some point). Christi captures the tone of Austen's writing in a wonderful pastiche that will leave you laughing and sighing.
Misappropriation of Lives by Milena D
SG-1 is kidnapped by Ba'al, but things get worse when the Goa'uld who once captured Vala wants her back. Dark fic in many ways, but also a strong Daniel/Vala story; there's a few authorial choices I mildly disagree with, but overall, it's a good read.
Operation Hide and Seek by Mara Greengrass
Jack, a small child, and the NID. It's not exactly what you think....
The Pegasus Connection by Nomad
An AU Atlantis crossover (season 8/1), in which dangling plot threads (including Ba'al and Jack's clone) are twisted together like taffy, and Jack gets to snark his way through two galaxies. Nomad's usual flair for plot and dialogue are showcased, and the characterization is just lovely. Novel length and an exceptionally fun ride.
Performance Review by redbyrd
Ever wonder what what Jack thought of the events of "Prometheus Unbound"? Give you a hint -- he's not happy. And Daniel is going to pay.... Wonderful, wonderful outside POV of Jack and Daniel and the sequel, Training Exercises, is even better. Definitely a don't miss. KikiRec
Shovel-bum by cofax
The always amazing cofax gifts us with a nifty AU -- what if Catherine Langford hadn't found Daniel that day? It's entertaining as hell to watch Daniel's mind work from outside the Stargate program.
Simple Addition by Philote
I miss Jonas, damn it. I'm still fairly bitter about losing him, and fic like this reminds me of that, but in a good way. A mission goes wrong (as always), and Jack finds himself alone with his new teammate and some old Issues. Solid Jack POV, Jonas comes off very nicely, and I really miss Jonas. < sigh >
Yet Another SG-1 Adventure by minnow1212
Jack heads back to Colorado to help out his team -- and it's for an even weirder reason than usual. Free-flowing lunacy involving all of the Season 9 usual suspects; you will fall over and die from giggling.
You Can Buy Her Things Now, But She'll Never Be Bought by minervacat
Daniel/Vala smut! Good Daniel/Vala smut! With contemplation and characterization and funny dialogue and did I mention the Daniel/Vala smut? Truly an awesome piece of writing, go read it now! NC-17
Home of anr, queen of S/J angst. The Twelve series is outstanding, The Grapevine is an utter classic, and there's just very little of the bad here. Here angst levels occasionally goes over the top for my taste, but her comedy can't be beaten.
AC's Stargate SG-1 Fanfiction
Fairy Tale is a sweet, realistic Sam/Jack story that captures both of them well, and dwells under no illusions. Plus, there are some great Teal'c moments. Start there and work your way through the archive; there is no bad.
More Daniel/Jack smarm and H/C, but Jmas also has a good handle on the rest of the team; read it all. Dammit, Daniel is particularly good, and Where Roads Meet is a great long fic.
The Barista by dietcokechic
A series of stories about a young woman with a talent for languages and ancient cultures, who works in a coffee shop near Cheyenne Mountain and forms a friendship with SG-1, particularly Daniel. You! I saw you roll your eyes! Trust the Perri. Kira sounds exactly like the worst kind of Mary Sue, and technically, she is. But she's also funny, compassionate, deeply appreciative of just how hot Jack and Daniel are, and oddly charming; if you start reading the epic, you'll probably keep going (it's actually not unlike eating popcorn). The chapters are executed around episodes; through Kira's eyes, we see the SGC from the outside, and how they interact with the Real World. It's not deep, but it is fun. Give it a shot, and remember that Mary Sue doesn't always equal EVIL. KikiRec
PHO's Stargate SG-1 Fanfiction
One of the consistently good authors in the fandom, divided between short episode continuations (This Is Getting Old is a favorite) and longer, well-plotted action fics (Mishap, The Past Remembered). Major Danny-whumping, and not inconsiderable Jack-whumping.
Out of the Badlands
Daniel/Janet has always been a favorite UC, and Little Red's Breaking the Code is sweet and fluffy and pointless and wonderfully true to both Daniel and Janet -- would that the series had gone this way. The rest is Sam/Jack or Sheppard/Weir, and very enjoyable at that.
In Sleepers, Alli Snow gives us a most excellent (and very long) Stargate fic, guaranteed to have you wondering whether you're coming or going. Another day, another planet, another Jack attack of PTSD... or is it? Intricately plotted, with fabulous characterization on Jack and Sam, and Teal'c and Jonas also play large, well-written parts -- I guarantee you won't figure it out before they do. Read it when you've got time to go in large chunks; you won't to put this down, and it won't work as well if you do. Trust me, it's worth the time.
My site, dedicated to Sam/Daniel fic, either 'shipper or friendship. Not too big, and closed to new submissions about a year ago (I'm not into the ship anymore), but most of it is pretty good.