Show: SGA
Rec Category: Alternate Universe
Characters: Rodney McKay/John Sheppard, Teyla Emmagan, Radek Zelenka
Categories: M/M
Warnings: Nil
Author on DW: siria 
Author's Website: Siria on AO3
Link: Woot Canow on AO3
Why This Must Be Read: Hopefully we're all relieved enough about recent events that we can cope with US political AUs again! In this short, amusing West Wing fusion, Rodney (Deputy Chief of Staff) has to fill in for Teyla (the Press Secretary) who's unable to do a crucial press conference due to... well, see the snippet below. As you'd expect, things don't go well! 

( snippet of fic )

Show: SGA
Rec Category: Alternate Universe
Characters: Rodney McKay/John Sheppard, Patrick Sheppard, Teyla Emmagan, Ronon Dex, Evan Lorne, Radek Zelenka, Carson Beckett, Cam Mitchell
Categories: M/M
Warnings: Nil
Author on DW: n/a
Author's Website: See AO3
Link: Beach Real Estate on AO3
Why This Must Be Read: This is a funny, lighthearted AU where John's a beach realtor and Rodney's new in town, a lawyer, and looking to buy. In only 3400 words, ficontessa creates a wonderfully recognisable AU, with Ronon and Teyla as John's friends, Carson patching him up, and Evan sorting out his disorganised paperwork. A big bonus is that Patrick Sheppard, while overinvolved, isn't a bastard or homophobic, and he and John clearly care about each other a lot. Plus, epistolary fic FTW and some outsider POV! It's cleverly done, and a great read. Ficontessa's a new SGA writer, so go leave encouragement!

( snippet of fic )

Show: SGA
Rec Category: Genfic
Characters: John Sheppard, Evan Lorne, Steven Caldwell, Elizabeth Weir, Ronon Dex, Teyla Emmagan, Rodney McKay, Radek Zelenka, several OCs.
Categories: Gen
Warnings: Graphic depictions of violence, minor character deaths.
Author on DW: domarzione
Author's Website: see the AO3
Link: The Jenny Code (the first of 3 fics) - on AO3
Why This Must Be Read: This is a series, with the main initial fic told from several POVs (Lorne, Elizabeth, Caldwell and Sheppard), then a companion fic from Rodney's POV, and lastly a brief coda from Sheppard's POV as he battles nightmares in the infirmary. The series is about a disastrous mission where Sheppard and several Marines are ambushed and captured by the Genii, after which Atlantis undertakes a rescue mission. There's a ton of plot and drama, focus on the harsh decisions leaders sometimes have to make in terrible situations, and on the values and heroism of the Marines. It's filled with excellent characterization, and, as expected indomarzione's work, features the usual cast of OCs - mostly marines, and Dr. Safir. As with all of the author's stories, there are bitingly realistic depictions of how the military functions - from strategy and tactics to internal politics and bureaucracy. The Jenny Code was reccd 13 years ago but the old link's expired and it deserves another mention. It's a tough read in places, incredibly well-written and very gripping. 

( snippet of fic )

Show: SGA/SG1
Rec Category: AU
Characters: Rodney McKay & John Sheppard, Jennifer Keller, Radek Zelenka.
Categories: Gen - McKay & Sheppard friendship
Warnings: no AO3 warnings apply
Author on DW/LJ: spike21 on LJ
Author's Website: most are on SGA flashfic on LJ, (or on DW here), with some on AO3, and here on McKay-Sheppard
Link: On DW: Part 1, Part 2, Part 3 - (or Part 1 on LJ - links to the next 2 parts)
Why This Must Be Read: This is a great "difficult reconciliation" and "forever friends" AU where the focus is on Rodney and John's estranged friendship, but there's also lots of gripping plot. Sholio reccd it a while ago in the H/C category, and that rec's very much worth reading. In this AU, the fork in the road is the end of S4 after 'Adrift', when John and Rodney never reconcile after the issue with Elizabeth being treated with nanites and the expedition founders and is recalled to Earth. Rodney hasn't seen John for a long time when he turns up at Rodney's house in the desert near Area 51 needing help, as the retrovirus changes from 'Conversion' have returned and are killing John. 
This fic is Gen and is complete in itself, but there's also a sequel written by Sarah_T, called you already know how this will end. It's John/Teyla, which is how Sarah_T rolls. 

( snippet of fic )

Show: SGA
Rec Category: AU
Characters: Radek Zelenka, Rodney McKay/John Sheppard, Elizabeth Weir
Categories: slash
Warnings: No AO3 warnings apply
Author on DW: n/a
Author's Website: Just on Wayback, these days
Link: Before & After on Wayback.
Why This Must Be Read: I'm a sucker for outsider POV, and Radek's voice in this is spot on, as he watches John not fully recover from being buggified in Conversion, remaining blue, with yellow eyes (hence the AU nature of the fic). Radek tells us about the problems arising from Earth and the IOA, and about Rodney going to bat for John. Heartwarming, and well written.

( snippet of fic )

Show: SGA
Rec Category: AU (Mensaverse, in this case)
Characters: Mensa!John/Mensa!Rodney, Aiden Ford, Radek Zelenka, and others.
Categories: M/M
Warnings: No AO3 warnings apply.
Author on DW: valderys
Author's Website: See the AO3
Link: The Fascist Mensaverse series on AO3
Why This Must Be Read: This is a fascinating dystopian AU which imagines a fascist Earth existing behind the Rod from the episode "McKay and Mrs Miller". It's from Dr. John Sheppard's POV - a far more paranoid and careful John than in canon. It's not cheerful, but there is a hopeful ending, and it's really well written, with great worldbuilding. There are two sequels that eventually take us up to the events of "McKay and Mrs Miller" from the Mensaverse's perspective. One interesting aspect of the series is that the Wraith aren't the worst enemy - they definitely have second billing. The ending of the final story is left open and at first seems a bit bleak, but if, like me, you believe Rod got back to the Mensaverse okay, then we can be sure he and John will find a way through together, with some help from their friends.

Here's the first part to get you started.

( snippet of fic )