Harmless by Shalott
Sheppard/McKay - awesomely funny and hot and clever. Cute and *very* friendly aliens get to know our heroes inside and out. It just make for one incredible image. This is what fanfiction is all about. And did I mention hot?
to Breathe by Speranza
Sheppard/Atlantis - Which might be the strangest pairing but it all becomes crystal when you read this story. Beautiful and vivid and very "scifi."
in Space by Torch
McKay/Sheppard - Witty dialogue, a little kissing and the stars. A simple and delicate story.
Below by Shalott
McKay/Sheppard - Shalott brings the sexy and funny like no other. So very hot and so very McKay!
Deniability by Sage
Sheppard/McKay - I think me and masturbation fic might have a thing. Or maybe it's just the too delicious thought of Rodney in the shower struggling with some alarming thoughts? Irresistable Mckay/Sheppard UST.
McKay/Beckett - There's a lot of Sheppard/ McKay in this fandom and, hey, I'm all for it, but if there was ever a story to sell me on another pairing then this is it. Philosophical and profound and one of the best pieces you will find in this fandom. The humanity given to Beckett and McKay is so touching and endearing you'll wonder why you didn't go for it before. Reminds you why you read fanfiction in the first place.
Eyes by Salieri
McShep overtones - Another brilliantly realised story. You're probably used to this sort of quality if you're already reading Salieri and you're totally missing out if you're not. Clever and creative with expertly written action and spot-on dialogue.
Some McKay/Sheppard - Not your ordinary fanfiction piece and some of you might have trouble appreciating it for what it is. However, if you're game, the concept has somewhat peculiar appeal. There are always many possibilities to the outcome of a story, what if you wrote all of them? A bit of a play on the idea of narrative as a fixed concept that leaves you with not so much a story, but stories. Clever and unusual. Give it a try.
Value by minnow
McKay/Sheppard. Minnow takes a rather cliched plot device (McKay gets telepathy) and turns it into a lovely, funny and insightful story full of warmth and terrific characterizations. She gives a fabulous Rodney and lovable Sheppard, and the rest of the gang in Atlantis are wonderfully fleshed-out characters in their own right. I'd recommend this story to anyone, even to those who usually don't read slash. Also? Minnow writes the best Zelenka in the entire fandom, like, my heart would burst out of my chest from all the love I have for this Zelenka--that's how much I love him. Go on, shoo! Go on and read!
The Taste of Apples by Auburn
Gen. A luxuriously plotty and meaty long fic, which reads like an episode, except darker and more complex. This story builds up slowly and beautifully, turns on its head several times, and proves to be richly rewarding at the end. One of the best stories I've read in this young fandom.
Legion the Things I Would Give to Oblivion by Auburn
More from Auburn, who's turning into a writer to watch for. Heed her warnings on top because this fic goes to some seriously dark, painful places, but never in a wallowing or gratuitous way. She does really interesting things with non-linear structure here, with the shifting timelines casting a pall over the proceedings from the very beginning. Lean, visceral, devastating fic, more so because it's quite plausible.
Necessary Things by minnow
Another brilliant story from minnow. This one is gen. It starts off funny and light ("Kavanagh, the bastard, wouldn't share his iPod with anyone") and gradually deepens into something moving and true. Such subtle touches, marvellously fluid prose, and spot-on dialog. *happy sigh*
Sheppard/McKay - Backstory, Antartica, hot sex and banter. The guys meet before the expedition to the Pegasus Galaxy and that just makes life complicated for two very complicated people. The story juxtaposes the lives of Sheppard and McKay, interspersing the present day story with events from each of their backgrounds. So goddamn appealing and clever and funny and compelling it will soon be a classic of the fandom.
by Contradiction by shalott
Oh, God. I love this story. I want them to film this and show it as an episode. Moreover, I think I might have just become a McKay/Sheppard shipper because of this fic. What does it have? Brilliant, funny, *pitch-perfect* dialog, kick-ass characterizations (not just of McKay and Shep, but of Weir as well), plus it's paced to an inch of its life, with plots, and hot, in-character smut, and did I mention the funny? Oh, my.
Referencing Gilbert Ryle by Brighid
Ah, personality downloads. Those can be pesky, especially if those personalities have feelings inconvenient to the owners of the bodies. This is quiet and melancholy and warm, as Brighid's stories often are. McKay/Sheppard.
Lost In Waiting by danVers
Post-"Storm", Sheppard gets captured by Kolya. Danvers gives a good Sheppard, and the interaction with Kolya is very believable. I really liked the prose-style, too, which is clean, sparse, and matter-of-fact.