About a Lamp by flambeau - this is one of those ones I always re-read for the way she builds this one in long and short scenes, surreal and just odd, but utterly, utterly amazing as they slowly fit together. There's a feeling of not-quite-right that everyone knows is there but no one can finger, and it opens up into a really fantastic Needful Things-esque type of story, in a fantastic way. Definitely takes the idea of careful what you wish for to a new and really fascinating place.
The Machinery of Heaven by flambeau - it took me two reads to really get it, but in my defense, pretty sure I had a bad cold. The plot is fascinating and complex and a couple of reads aren't any hardship at all. Rodney's engineering skills are needed to help fix a machine, but not everyone on the planet wants it restored. It starts slow and easy and moves faster the farther in you get. Did I mention bracelets for thought sharing? Yeah. Just like that.
Intersections by kaneko - first season canon based, a vaguely alternate history of John and Rodney's first meeting and their respective pasts. Moves between past and present flawlessly and one of my favorites for random re-read.
Instantaneous by Cimorene - personal transporter! Mostly. Inspiring scientific exploration, long jumper rides, John learning the art of startling people for fun and profit, and an interesting exploration of the possibilities of use.
The Pegasus Device by liketheriverrun - very WWII AU of Private Detective John Sheppard and criminologist Rodney McKay. Oh heck yes. With mysterious deaths and strange accidents and the war coming home. It's so totally a great fannish caper and it. Is. Awesome.
The Taste of Apples and Sacrificial Drift by auburnnothenna - novel and sequel, start with gen that becomes slash. A great plot for the first part that grows creepier and odder at every turn. Mindlinks and alien spores and do not want to spoil, but must be read. Very awesome.