Pretty much straight gen here; I go for team fic and action/adventure more than anything. Just a few McShep stories, which are so good you've almost certainly already read them.
Created as the archive for a slash-only mailing list, their gen category contains some of the best of the best, and there's a wide range of shiper fic available as well.
Some Element of Repetition by EllieV
Ford fic! Ford fic! Really good Ford fic, post-Hot Zone, that shows him as the young, fairly inexperienced lieutenant he is instead of the uptight Marine we used to see on-screen. Most of the story is a conversation with Sheppard that is perfect, and gives us some fabulous insight into John as well. God, I love this fic! (The companion story is Sheppard's POV and almost as good. Although Beckett's notes are the best part.)
Underneath by Elnea
A neat little adventure story centering around McKay and Weir -- it's not a common match-up for adventures, but Elnea pulls it off nicely, making both characters pull their weight. McWeir-ish, but it works with the story.
Woobies of Woe by AbylityMaren
AbylityMaren classifies this as "anti-kid fic", and she's really not kidding. McKay gets stuck with the care and feeding of a traumatized two-year-old when her home is destroyed by Wraith. McKay is not happy. Neither is the two-year-old. And they're going to take it out on Atlantis. Read it somewhere where people either won't notice or won't care when you begin snarfing liquids all over your monitor and cackling in evil glee. (When Legion leaves you collapsed in agony, go read this. Guaranteed antidote. Because I'm a nice person.)
An off-shoot of the main Stargate archive; there's a lot of duplication between this and other archives, but you might get lucky. Also try Heliopolis 2 for adult fic.
Stargate: Atlantis @ Fanfiction.net
Yadda yadda, horrid drek-to-gem ratio, yadda yadda, slash and shipper-heavy, yadda yadda. As always, if you take the plunge, I recommend finding authors you like, then following their Favorite Authors and Favorite Stories recs, as opposed to trying to wade through unguided. Good luck.
Kodiac Bear Country
Mutiny on the Caritas is a Ronon first-person POV, believe it or not. A fast-moving plot involving kidnapping and a slave ship is pushed along by a Ronon-voice that rarely falters, resulting in a very solid team + Beckett fic that has no business working as well as it does. There are few punches pulled on a couple of interrogations; tread lightly if you can't cope, but it's so worth the ride.
The Geeks and Goons series (starting with Scientist, Wraith Killer, Space Pilot) gifts us with some of the funniest (and occasionally most touching) Sheppard/McKay interaction in the universe. The characterization on both men is pretty accurate, the byplay screamingly funny, and Sheppard's thoughts on McKay resonate nicely. Non-slash (except for one marked story); lots of whumping, but definitely not one to miss. The Cassandra Effect is a silly piece written in the wake of the rumor of an SG-1 cast member joining Atlantis (no the confirmation kerfluffle. Very silly, mostly because it's all true. And did I mention silly?
liketheriver's POV series is a little tell-don't-show on relationships for my taste (and just too meta in spots), but she's mostly overcome that by the time she hits Games. By a few pages in, you'll be giggling helplessly and trying not to fall off the chair -- she nails Teyla's POV (a neat trick) and everyone else's voices, and the situation she gets our merry team into is both suspenseful and hilarious. Give it a try. (Steady State is also very solid; actually, her entire Dictionary series starting with Redux is worth your time.)
Under Glass is a fun adventure story (complete with her requisite whumping), but also a quite good teamfic, with Teyla and Ronan getting their share of the spotlight. A solid read, as is most of her stuff. I meant it about the whumping, though.
The "voyeurism" challenge on sga_flashfic produced the expected amount of smut, but also a few real gems, like More Than Enough, a Bates POV offering. Besides being a great visit inside Bates' head, it's also a remarkably strong portrayal of Sheppard and Teyla's relationship, which works even better for being seen from a very unexpected, and very unfriendly, viewpoint. When The Kittens Have You is quite different, but very entertaining -- give pretty much everything she's done a shot.
Don't let Sheppard and McKay loose in an ancient temple. Because there's giant axes and Wraiths and ghosts and traps and... yeah. Just don't do it. Tipper spins a wonderful ghost story in Bioluminescence, with perfect dialogue, great character interactions and just the right touch of the supernatural to leave chills running up your spine at the end. Thieves in Atlantis is also a solid adventure, set on Atlantis herself; a little heavy on the whumping, but there's a strong, absorbing plot, and everyone has something to do. Almost anything by Tipper is at least readable and usually entertaining.
The Common People Challenge
CL Kamnikar reimagined an old X-Men challenge, to take ordinary, everyday people and give a glimpse of their lives in an extraordinary world. Lots of gems, including Mara G's Ordinary People.
Don't miss a word of LTLJ's fic, but start with the Retrograde series; a brilliant crossover with SG-1. The Daedalus shows up on Atlantis... three years after the expedition left. Problem is, they're about two weeks too late, and Atlantis has been invaded -- by Earth. LTLJ systematically nails each of her characters; Jack and John are particularly brilliant, but everyone gets at least one really great line. It's the details that really make it, though; Atlantis seen through Jack's eyes is a very cool thing.
City on the Ocean's Edge
Sholio gives awesome team fic and equally awesome Sheppard and McKay buddy fic. Read it all, seriously. Go now.
Postcards to Jeannie
The classic trope of correspondence fic, given a neat twist by the use of gorgeous illustrations. Postcards sent back and forth between Jeannie and Teyla, with the rest of the team pitching in (you can tell by the handwriting). Some excellent character moments, particularly involving Rodney; alternately touching and quite funny.
Running on Empty
This takes a great concept -- McKay and Sheppard implanted with Wraith transmitters and on the run -- and turns it into an adventure novel that never stops moving. Wonderful characterization throughout, she avoids nearly all of the melodramatic potential without missing any of the emotional impact, and she introduces a gang of OCs who are utterly delightful. Give yourself some time with this one; you won't want to put it down. Then go read absolutely everything else she's written.
The earliest days of the Atlantis expedition, and McKay and company struggle with that most essential element of survival -- getting the bathrooms to work. As usual, Sholio's touch with character voices is right on; drama and humor are interwoven nicely.
Wraithfodder has put together some of my favorite Atlantis stories; I'm not as in love with the episode continuations, but the original stuff is awesome.
I've Got You Under My Skin
Whumping heavy, but also characterization heavy, wth none of the melodrama that usually accompanies whumping. It's novel-length, tight and plotty, and everyone gets something to do. Definitely rocks my gen-lovin' world
Another good one from Wraithfodder, as Sheppard takes his team out for a day of target practice and training on a very boring planet. Of course things go Horribly Wrong. Hugely entertaining chaos ensues, as well as good early team bonding.
Of Memories Past
More team bonding (including good McKay and Teyla, which no one ever does!), and some fun, WAFFy goodness.
Home of Auburn's fabulous fic. She does some weird things I haven't read, but these two stories are brilliant, so you might the like the others.
Legion the Things I Would Give to Oblivion
Auburn seems to be trying to traumatize us as much as possible, and she's succeeding. Dark, dark, dark fic, but detailed and gripping. To quote her summary, "The Wraith are many and the Daedalus is just one ship. Things go very, very badly." Yeah. You'll want to reread this a few times, just to appreciate all of the little things (and the huge honking painful stuff) and get everything in order in your head (so it can hurt more). SG-1 makes an appearance, and there's one other crossover that works in an incredibly cool and perfect way. Read it, now, but have happy!fic (see Woobies of Woe above) ready after you finish. Trust me. (Slash/threesome alert, but it's peripheral and not-explicit, really only there to amp up the pain, and succeeding in doing so. Ouch.)
The Taste of Apples
Not a happy fun fic, but a thoughtful, often painful fic, one that takes time on the details and skims a bit over the big picture, to stunning effect. Another planet, another strange life form, but suddenly Sheppard's team is in a new, weird, and dangerous place, and the rest of Atlantis has to decide how to deal with them. Precise characterization and observation that will suck you into the story like you wouldn't believe. (There's a sequel that's quite good; slash warning.)
In Flying Blind pulls out a story of a first contact gone horribly wrong, does it from everyone's POV, and methodically nails each and every one. In the process, she deals with the traumas of first season and takes us into second season and all its possibilities without giving away more than one semi-spoiler. One of the best Atlantis fics I've run across -- just awesome. Other awesome work from Minnow: Seven Ways John Sheppard Goes Home, Necessary Things, On Bad Days, John's an Optimist
Domenika Marzione takes a unique approach to Atlantis fic -- she writes primarily from the POV of the military, giving Atlantis an entirely different set of military details that tend to get glossed over in fic (and on the show, actually) A lot of Sheppard and a lot of Lorne, as well as the gang of wonderfully realized OCs who comprise his off-world team. And she does it well. The Jenny Code is a good place to jump in, to meet her Lorne and his merry gang, but leave yourself some time; it's a good, solid, longish story and you won't want to stop once you start.
Ars Arboreus by Mahoney
A fabulous team adventure, with another first contact gone wrong and a really alien culture. Deeply cool world-building, everyone gets something to do (including Elizabeth!), and Mahoney somehow creates one of my favorite OCs without it ever uttering a word. Plus there's action and snarking and great dialogue. Definitely a must-read. (Also try Stick Around for some more suspense.)
The Art of an Atlantis Mission Report by Jem
Ronon meets mission reports; Elizabeth is unamused. Ronon and Sheppard are highly amused.
Athosian for Beginners by trinityofone
Nobody understands how the theoretical translation software of the stargate works, but think of the havoc if it suddenly cut out. Quite good Teyla POV on Atlantis and coping with being suddenly very alien; some interesting observations and characterizations.
Barbados by Chrissie
Everyone needs a vacation sometimes, no matter what it takes to get it. A solid team-bonding story, with a cool structure that carries you through the story even when not a lot is happening (which is kind of the point).
A Beautiful Lifetime Event by shalott
Slash has to impress my socks off to get me to finish it, much less rec it. A little lab accident lands McKay and Sheppard with a new addition to their lives that changes, you know, their lives. Everything works --Sheppard's POV is perfect, and things develop so rationally that you're yelling at the pair of them to just sleep together, already! by the end of the story (if you're not too busy giggling or sniffling). Does get explicit, but not until the very end, and it's easy to bail if it's not your cup of tea. Give it a shot.
de profundis - up from the depths by agentotter
An utterly, utterly adorable story set after the events of Grace Under Pressure. The Rodney voice is far too good, the 'day in the life' aspect is detailed and hilarious, his reaction to a visitor is just awesome, and you will be grinning like crazy when you finish. Also try a capite ad calcem - from head to heel ; to quote the author: "I was getting all cranky at stories that make Rodney out to be a total sensitive flower about his weight (which is, I'm deeply sorry overly dramatic fiction writers, perfectly average and not morbidly obese)." True and true, and the result is a quite funny little first-season team fic.
Displacement by smilebackwards
"John isn't really sure how to feel about the fact that he seems to have been unofficially adopted by SG-1."
Exigencies by Rivier
A shuddery dark fic, told entirely through the eyes of an original character, that works brilliantly. Just how far would John Sheppard go to get back what someone took? Answer: really, really far. Tight and chilling (warnings for violence) and very good. (Rivier has reopened her LiveJournal, so this is available again.)
Four People Who Got the Job (and One Who Didn't) by 2ndary_author
Five vivid character sketches of interviewees for the Stargate program.
Free 'Verse by dashamte
"Look, you're an ass and your equations don't work, but you do deserve a hamburger." Rodney on Earth, coping with Ancient poetry and Samantha Carter -- and having suprising success with both. A cool back-home fic; dashamte keeps all of the history, but allowed for the changes in Rodney without getting sappy about it, with awesome characterization of Carter as a bonus. I'm not sure how well the poetry thing actually works, but it's a cool idea.
freedom's just another word for nothing left to lose by synecdochic
Astonishingly and astoundingly beautiful future AU (we hope) for Rodney after the Atlantis program. The story and the backstory are built beautifully, and Rodney is exactly as he would be given that backstory. Simple, clear, gorgeous prose that just makes my heart hurt, even as a little hope sneaks in. Slash around the edges, but it's so not the point, and you'll barely notice except where it hurts. I think I stopped breathing about 10 paragraphs in, and didn't start again until long after I finished reading. (To recover, try her Rodney McKay Is a Very Bad Manager, a short and killingly funny response to the Documentation challenge on sga_flashfic. You'll have to download a Word file, but it's clean and more than worth it.)
Fresh Blood by tigs
A wonderful (quite AU) McKay perspective on the aftermath of The Seige; the portrait of Atlantis is damn near perfect, the situation and Rodney's emotions are both plausible and heartwrenching. Also try The Long Way Home, a well-written Lorne POVs, on an away mission with Sheppard's team to a place in Pegasus that actually likes them. Beautiful extrapolation of the character.
Hero for a New Age by smittywing
Comic books as metaphor as comic books -- brilliant Ronon insight as McKay introduces him to Batman and the Fantastic Four, and we learn about the stories of his world, as well. Wonderful interactions with McKay, and great bits with other Atlanteans.
Heteronormativity, Gender Construction and Nonverbal Signaling in Intercultural Communication: A Comedy by mad_maudlin
John thinks Teyla is trying to kill him... by feeding him. Or something like that. A brilliant extrapolation of the Mensa AU: hilariously detailed, sometimes sweet, and totally off the wall in spots. And it's John/Teyla, which isn't what you think it is in this universe. KikiRec
Hindsight by Pru
This fandom is ruining my reputation -- I keep reccing slash. But damn, this is just an amazing AU, with a John Sheppard who is just like the John we know, with one difference that changes everything. Rodney, of course, is supremely Rodney -- with one difference. Slow and serious and funny in the best possible ways, and by the end of it, you will not only believe, you will beg for more.
Hockey Night on Atlantis by canadian_snoopy
A freewheeling, fast and funny fic about a hockey tournament in another galaxy. Rodney's POV is the perfect narration for the Stanley Cup for dorks, and the use of original characters to fully field the four competing teams is truly a thing of beauty. (Also try Variations on Loneliness, another fine product of sga_flashfic, and a lovely Teyla POV. Cleanly but poetically written, and her growing relationship with someone unexpected is believably portrayed.)
The Illustrated Rodneysaur by Moonloon (illustrations by Spaggel)
< giggling > Okay, this fic is not to be taken seriously, but it is to be enjoyed entirely. Because if Rodney were accidentally turned into a small green dinosaur, this is exactly what would happen (well, if everyone was British, because Moonloon's dialogue slips occasionally). Plus, there's the added benefit that you will totally be ded from cute.
International Relations by Melyanna
A really well-done AU, featuring a John and Elizabeth who meet in Kosovo well before the Atlantis project. Their straightforward romance proceeds through seperation and disaster, avoiding melodrama or sappiness all the way through and sliding seamlessly into the events of "Rising". Just awesome. (The link is to part 4; links to parts 1-3 are at the top of the page.)
Instructional by Seperis
"New personnel may bring bad habits to resident personnel, yes? Go here, go there, do as told, shut mouth. Very annoying. Perhaps they need reminding of peace and harmony in Atlantis when all goes smoothly." There's a learning curve on every base and the new military arrivals on Atlantis are about to learn some lessons, courtesy of McKay and the science team. Not great art (and written before we got to know Lorne), but funny as all hell; John is resigned and amused, Zelenka is Satan's right-hand man, and Rodney is at his vindictive, evil best.
The Laundry Ultimatum by explodedpen
From the Stargate genficathon, the story of the bravest man on Atlantis. :)
The Law is an Ass by derry667
Sheppard's team encounter the donkey-worshipping inhabitants of M4S-291. Warnings for lots and lots and lots of puns and really juvenile, lame-ass humor. < snicker >
Logically Irrelevant by miera
Yes. Oh, yes. This is how John/Elizabeth should be written. The emotions and interactions come across just perfectly, absolutely true to both characters. The pacing is perfect, the romance sweet without being even slightly sappy. Oh, this works.
The New Frontier by Sarah T
A fantastic pastiche of "Shane", starring a Lone Stranger named John. The OC narrator is really well done, with a strong and consistent voice; the homage captures the spirit of the old Western without being limited by it. Little moments here and there stand out beautifully, and John will absolutely break your heart. (For something entirely different, Be My Homeward Dove is a gorgeous Elizabeth Earth-side fic, the trio bonding after John's promotion. A funny, thoughtful, almost sweet story.)
On the Road to Come What May by Eildon Rhymer
"It started with a strange vessel crashing down from the sky. Then three strangers appeared in a decaying city, willing to risk everything to rescue an injured, imprisoned friend. For those caught up in the adventures of these four, nothing will ever be the same again." Novel-length, in outside POVs only.
The Pegasus Connection by Nomad
An AU SG-1 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.
Pilgrim's Progress by sardonicsmiley
"You're not God, Sheppard's not your messiah, and I'm not the anti-Christ. But I am going to kill you." Phenomenal Rodney and Teyla team fic, facing down a 'religion' that threatens Atlantis, the Athosians and possibly the whole galaxy; creepy as hell in the best possible way.
Relative Positions by Merry
Part of the Flashfic First Night challenge, Merry gives great McKay and Sheppard bonding. The dialogue is excellent, the inside of McKay's head rings perfectly true, and the offer and acceptance of a place on Sheppard's team is very nicely done.
Somewhere I Have Never Travelled by Brighid
Oh my god. What "Beneath the Surface" did for SG-1 (amnesiacs given different identities), Brighid does for the Atlantis crew here. Half the fun is guessing who is who -- all of the pain comes from finding out. Beautifully, beautifully executed, poetic and heartbreaking. Kikirec (Also try her
Smart, which has close to the best Rodney characterization ever -- lines here and there keep breaking my heart because they're so damn perfect.)
The Stars My Destination by Mad_Maudlin
A phenomenal fusion of the Stargate Atlantis charcaters into the Star Trek: AOS universe; the Atlantis characters mirror the Trek characters without ever losing themselves, and the twists and turns of the plot are familiar without being predictable. KikiRec
The Start Line by sdraevn
Ronan-fic! And good Ronan fic, contemplating silence, Atlantis and his new team. and whether he wants any of them. His take on McKay is particularly perfect, but I love all of this.
The Strange Case of John Sheppard and Elizabeth Weir by A.J.
A little bit of body-swapping fluff. It's not deep, but it is entertaining; the dialogue is spot on and the little details are nice.
Stuck! by kolyaa
Kidfic! Yes, I know, but this one has a higher than usual measure of funny, adventure and angst, and a quite low schmoopiness content. Also, Rodney as a 4-year-old? Too much fun. And since most of Atlantis is involved at one point or another (with quite good characterization), it has many more points in its favor. Give it a shot.
The Towers On The Heights Reach To Heav'n's Own Blue
In which John Sheppard hates cricket and accidentally starts an intramural soccer league, and Cameron Mitchell thinks McKay's sister sucks. Hilarious fic centered around email correspondance between Mitchell and Sheppard; not quite a slice-of-life, but no one gets shot, either. Unfaltering John POV; it'll help if you know college sports, but not a lot. :)
Where You Hang Your Hat by destina
Sam Carter on Atlantis, but still connected to home.
Windswept by cofax
A neat little John POV of a solo exploration of the city in the first weeks of occupation. Nothing much happens (which is pretty much the point); the language is beautiful and little moments here and there just get you.
Words by The Moonmoth
I'm a well-known sucker for a well-written Rodney character piece, and this is a lovely one. The situation is given to us in bits and pieces that set up Rodney's state of mind without disturbing the flow of his thoughts. The inside of Rodney's head rings perfectly true, and his interaction with Sheppard is right on.