1) He learned Russian in college, just in time for the end of the Cold War. He's never really had a practical use for it, but he did discover while at Stanford that he rather liked the literature, so every now and then he'll pick up a copy of something by Pushkin or Tolstoy or Dostoyevsky in the original Russian, just to keep his skills up. The copy of War and Peace he brings to Atlantis is one of these, with a dust jacket taken off a translated edition. Even then, he knows it doesn't look like your average flyboy reading material, but it's a lot easier to tell the people who notice it that he wanted something that would take him a while to read rather than admit to liking Russian novels.
It becomes a running joke among the members of the Expedition who know about it that, for all his reading, he never seems to make any progress. But that's not true. By the time the city touches down in the Pacific, John's read it through seven times.
2) He wasn't the one to cut off communications with his father. John wrote home every birthday and holiday for five years after he first joined the Air Force. His father just never wrote back, despite the fact John made certain to let him know of his new address – and the phone number he could be reached at – for each new posting. Patrick Sheppard only wrote back once, to the letter John sent him about getting married, and even then the letter was addressed, not to him, but to Nancy. After he gets divorced, John doesn't even bother trying to keep in touch.
The last time he talks to his father, it's to tell him Nancy's filing for divorce. His father hangs up on him and dies of a heart attack nine years later.
3) He was married to Nancy for three hundred and thirty-three days. She's the sister of one of his buddies in his unit. She's barely old enough to drink when they meet in a bar outside Boston, and he proposes her three months after that because it seems the thing to do when he's just found out he's being transferred to Ramstien soon. Things go south, however, not long after the move to Germany, and she flies back to the States without him one night while he's in the field sometime during week twenty-three of their marriage. When he makes no move to come after her, she files for divorce. (She claims that the man he is in private is too different from the man she met in the bar outside Boston for her to stay married to him. That the man he is in public can smile and laugh and joke with the best of them, but, in private, when it's just the two of them, it's like they're a pair of strangers who just so happen to live in the same house for all they talk to each other.)
The last time they talk, before running into each other at his father's funeral, she says she doesn't think he's capable of loving anyone. Not in any way that matters. That's he's just too solitary a person to be capable of it.
4) He loves to fly, but it wasn't his first passion. Math was. He loves the order of it, the logic. It doesn't lie, the way people do. Something is either the answer or it isn't, and, if it isn't, then the fault's somewhere in the solution and easily fixed. Sometime in high school, however, he realized that there were more career options for a pilot who liked math than a mathematician who liked to fly, and so he decided to join the Air Force.
Sometimes, though, John still wishes the world worked a bit more mathematically. Because then he wouldn't have had to go alone, against orders, to rescue Holland and the others (because we don't leave our people behind was a universal constant). Because then the natives of the planets they visit throughout Pegasus wouldn't be so hostile (because if people of Atlantis = enemies of the Wraith and people of Pegasus = enemies of the Wraith then people of Atlantis and Pegasus = allies against the Wraith, or ought to). Because then they could have saved so many more.
5) He loves Rodney. Which isn't so much a secret (most the Expedition has figured it out by now) so much as why he loves him (which, sometimes, not even Rodney knows). But he does, because it's hard not to love someone who's risked his life for yours, even though he's scared, and who doesn't care if John's more than a bit of a geek in his own right, or if his job has to come before their relationship, or if he's truly horrible at relationships, especially those he tries to make work.
Because Rodney apologized (when he never, as a rule, apologizes for anything) for what happened on Doranda.
Because he didn't treat John any differently when he was turning into the Iratus-hybrid.
Because he didn't care what hour of the night (or day) he called, wanting to talk about everything and nothing, during their six week exile on Earth.
Because, in an alternate timeline, he spent his entire life trying to find a way to make sure John was never sent into the future to begin with.
Because, when Rodney couldn't remember anything at all, he could still remember John.
Because, no matter how much time they spend together, they never get tired of each other.
Because, no matter how much they fight, they always make up.
John loves Rodney because, even when there are still other people, it's always them. And if that isn't love, well, then he doesn't want to know what is.