ltlj or miss_porcupine tend to have, to me, the clearest and most accurate John characterizations in the entire fandom. Any of their fics pretty much conceptualize how I see the character. I'd also go with samdonne as another one that writes a devastatingly accurate John Sheppard, able to balance John as both a person who has some fucked up in his life with someone who is canonically very competent and intelligent. A lot of fandom, to me, puts a lot more value in wahtever they are reading into John's issues than the character himself.

But one story for John characterization--Retrograde by ltlj

Um, okay, for slash. Hmm. Closest I'm going to be able to get is cesperanza, but then, she feels like one of the few slash writers who genuinely likes John. She tends to hit me right most of the time, and even when she doesn't, she's good enough at building the story that I buy it completely while I'm reading it.