This, for instance, would be a few of my 'John Sheppard doesn't really understand himself, but that's okay' recs:
Nondisclosure Agreement by synecdochic - Okay, she's best know for Freedom's Just Another Word For Nothing Left To Lose, but I'm sure everyone's read that already. This one's a gorgeous John gen piece, detailing where he's been, where he is, and where he's going, in a format that gives away a lot and almost nothing at all.
11. Sometimes John sneaks out to the east pier, to the part where the steps lead down into the water. He takes off his boots and rolls up his pants and puts his toes on the last step, the one covered by an inch of ocean. The water is always cool but not cold, and it makes him think of lemonade and rum drinks with umbrellas and the shining silver joy of catching the one perfect wave.
recognized none but the southern cross by minervacat - This is short, but the author uses the space well, painting a vivid picture of Atlantis and John and Rodney. It's achingly beautiful and achingly true.
Rodney calls the first star, the brightest star, Polaris, and when John goes to shove Rodney away he ends up with his hand curled against the line of Rodney's jaw, and Rodney's mouth feels like home.
You Inevitable Unhappy Ending by helenish - John and Rodney and miscommunication mishaps of the entirely too human variety. It's sweet and awkward, and John really doesn't get himself at all, but it's really okay.
It wasn't the first time he'd had an idiotic crush on a guy, but it was certainly the most inconvenient. Lucky, then, that Rodney never noticed, not even when John timed dinner for two months so he could eat sitting across from Rodney, not even when he found excuses to touch Rodney, shoulder, elbow, chest, once, not even when he took Katie Brown on four dates and tried to fall in love with her because Rodney had liked her.
Kid A by cesperanza - John comes to terms with relationship with Rodney. It's a sharp, intelligent look at John and his variety of issues with a hint of sweetness.
So he overcompensates, goes too far the other way, saying cutting things to Rodney when they're offworld or in front of other people. Rodney seems to know what he's doing and just rolls his eyes.
No one thinks he's gay. They just think he's an asshole.