Things to Do in Denver When You're Dead by cesperanza - Gorgeous, GORGEOUS McShep piece about their post-Siege visit to Earth. It breaks your heart and then stitches it back together with love and symphony and football and cats. Oh oh oh.
Nothing else but the mysterious pull of the moon by mirabile_dictu - Epic, multipairing futurefic.
Freedom's Just Another Word for Nothing Left to Lose by synecdochic - Literally one of the best pieces of fiction I've ever read, period. Rodney, future-fic, post-Atlantis, with implied McShep. It's gorgeous and heartbreaking and is guaranteed to make you cry.
Transcendental by astolat - Epic story that feels like a particularly fantastic two-parter episode. Features the Genii. Entertaining and hot and just fabulous.
Bell Curve, or, Ladies' Night at the Boom Boom Room by rageprufrock - Long AU McShep. Hilarious and wonderful. Also the first story I ever read in this fandom, and it left no question - my soul was sold :)
String Theory by toft_froggy - Another long AU McShep :D I like those. This one is really emotional and poignant and quietly gorgeous.
Alpha Centauri by hth_the_first - A wonderfully complex and fascinating and HOT John/Rodney/Ronon. So so good.
A Farm in Iowa by sheafrotherdon - A beautiful, perfectly characterized McShep AU (I told you like those! So does this fandom :)) that just makes me sigh with happiness. Everything else she's written is wonderful too.
Ardhanaraishvara by auburnnotlisa - Genderswap that's not crack! This story takes a tired fic cliche and turns it into a fascinating psychological study of every one of the team members, looking at gender roles and identity and all kinds of thinky things. I haven't even finished it, as it's something insane like 200k words, but it's like reading a great novel, you can pick it up and put it down at any time and always want to come back. Well well worth it!
Other Comprehensive Rec Lists
Gigantic page of recs - I haven't even begun to break into all of it. It's not all McShep, but plenty is.
Ridiculously fun and awesome rec list format
- siriaeve ( http://siriaeve.unrealwords.com/
- lamardeuse (http://lamardeuse.dreamhost.com/sg/
- astolat (http://www.intimations.org/)
- rageprufrock (http://glitterati.talkoncorners.net/
- cesperanza ( http://www.trickster.org/speranza/
- shrift (http://bifictionalbedlam.slashcity.
- thegrrl2002 (http://www.geocities.com/thegrrrl2002/
- Resonant (http://www.trickster.org/res/#sga)
- aesc, dogeared, scribblinlenore
My McShep memories - Includes many stories from authors not mentioned above, whose stories I often didn't memory because they were off LJ.