The main problem doing this is wading through the sheer volume of fic out there. There's AU's, episode tags, character studies, mission fic, and the ton of fic that reads like crack but isn't because this fandom is so completely mental. (In a very good way).

I have two:

The first is an AU with a slightly different Atlantis, in a society where everyone is divided into Tops and subs. It's very kinky and very hot, but yet, the characterizations are dead on. It's one of those brilliant stories that might not be suitable for someone new to the fandom, who wouldn't get all the interactions. But . . . teh sex. Whoa.
Coming Home by Xanthe

It has a sequel here: General and Dr. Sheppard

My second rec is easier for people new to the fandom, and although it's a Season One fic (Ford is present), it's brilliant. There's the relentless pursuit of coffee, there's weird alien sex practices, there's John with butterflies, mystical links, and all sorts of goodies.
The Machinery of Heaven.

Hope you enjoy 'em!