The only factor that doesn't change is his SO (significant other).
Main/Default - This is more canonized (at the mun's discretion). But this 'verse is open to anyone and everyone. His SO in it, however, is General Jack O'Neill.
An Ancient Joke - During the course of investigating certain unexplored areas of the city, Dr. Rodney McKay and Dr. Radek Zalenka who are escorted by John, run into a peice of Ancient tech that they've never seen the likes of. Apparently the idea of curiousity killing the cat doesn't play a part in their thoughts and they investigate. After going into the room, John's presence activates the device, due to him carrying the ATA gene and emits a particularly bright light, followed by a 'pulse' of some sort that seems to have been directed at Sheppard. Nothing happened that can be detected by either scientists or Dr. Beckett.
The device acts on subconscious desires and if need be, changes physiology subtley to compensate. The Major's subconscious desire? To one day have a family of his own. He goes home for the holidays and spends time with Jack. The results of those subconcious desires come into place after that.
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As for John's recent 'expedition' to an alternate future of Atlantis, that is not his verse, hence why any characters that ARE from that verse are tagged as such, and John being tagged as [stuck in] when reffering to the citrus-free verse of play. Any verses he visits that are out of his 'realm' of usual play, will be tagged as such, but they are not his.
Any questions pertaining to the aforementioned verses that are not his own, should be directed to the regular players of that verse.