Sheppard/McKay established, Sheppard/McKay/OFC one-shot.
Five years after Atlantis, John and Rodney meet someone interesting.
In Between by
McKay/Sheppard/Dean Winchester one-shot. McKay/Sheppard continuing & past Sheppard/Dean implied.
Two days, four men, one California King mattress. Sometimes two and two can add up to something more. House cross-over.
It Takes Two by
McKay/Sheppard/Norina (from "Inferno")
Criminal Minds crossover. Star Trek drinking game with another genius leads to some unexpected fun.
"And now they’re having their picture taken together. What is this, the prom?" House cross-over.
Pegasus B by
An AU universe with several off-shots. One of them is Daniel/Rodney -> Daniel/Rodney/Sheppard -> Rodney/Sheppard & Jack/Daniel. See the Pegasus B Story Guide.
Sequel: Rhowch eich dwylo ar fy pen ôl. Crossover with Torchwood. McKay/Sheppard established, McKay/Sheppard/Cpt. Jack Harkness first time.
Crossover between Stargate Atlantis, First Monday (where Joe Flanigan played Julian Lodge) and Boa vs. Python (where David Hewlett played Dr. Emmett). McKay/Sheppard and Lodge/Emmett are the main pairings, but the series also features McKay/Lodge, McKay/Sheppard/Lodge & McKay/Lodge/Emmett.
Soft Swap by
"What's the Guinness record for number of vampire-human simultaneous orgasms?"