In post-Reichenbach fics, Sherlock sometimes dyes his hair red while he's pretending to be dead.
Sherlock's eventual reunion with John post-Reichenbach is normally after three years (as it was in the novels) and John either punches Sherlock, kisses him, or faints (depending on whether or not the person is a shipper and if they've read the originals). As it turns out, it's two years, and John first punches, then headbutts Sherlock.
John also seems to have a jam fetish.
Upgraded to canon (sort of): a jar labeled "John's Jam" appears on Sherlockology's "Silver Blaze" advent calendar.
Lestrade apparently got Sherlock off drugs as a condition for letting him consult.
It's commonly accepted that the Holmes family is very, very rich. Many stories involve the "Holmes Estate". However, the story "His Final Vow" shows Mr. and Mrs. Holmes living in a cottage in the country—not exactly a mansion.
Along with this goes the notion that the reason Sherlock needed help paying the rent is that before the consulting-detective business became lucrative, his income was from a trust fund which was under Mycroft's control.
John's father was either an alcoholic, a soldier, or both.
Lestrade has a young daughter.
John's leg injury was real, but not from a gunshot. Also he has recurring pain (and sometimes limited mobility) in his injured shoulder.
John, as he said in "A Scandal in Belgravia", is "not actually gay" — but neither is he completely inexperienced with men.
There's a recurring motif in fanart that John has the RAMC insignia as a tattoo.
For some reason, there seems to be a widespread joke/belief involving John and red underwear. In other words, avoid Tumblr on "Red Pants Monday" if you aren't a shipper. And apparently Martin Freeman knows about it, too.
Mummy Holmes is either an Alzheimer's victim or M. Going by her appearances in Seasons 3 and 4, she's definitely not the first.
Many fans treated SebastianMoran as a regular character in the show long before he actually put in an appearance in "The Empty Hearse". Most fans assumed that he'd be a faithful modern update of the character in the books, though Sherlock's Moran (a crooked MP in the House of Lords, who acts as The Man Behind the Man to a terrorist group) turned out to bear very little resemblance to Doyle's Moran (a former Great White Hunter who acts as Moriarty's personal assassin).
John is never seen making tea. Sherlock makes it.
Sherlock says that "Mycroft is the British government, when hes not too busy being the British Secret Service or the CIA on a freelance basis." Fans have taken this to imply that in addition to the British and American intelligence services, he runs basically every intelligence service on the planet. There's no evidence to support this, but then, there's no evidence against it, either...
"John, we're out of milk." Explanation: The number of fanfictions mentioning milk (or rather, the lack of it), is astronomical. In universe? It's mentioned once. (Well, technically twice, if you count Sherlock'sforum.) Three times once you find John's private blog.
Also, "John, could you pass me a pen/my phone?" works as well.
Either of the two above followed by -SHExplanation It's become very popular within some areas of the fandom to roleplay as any combination of characters from the show on Omegle. The milk line is frequently used to start off the conversation, and the character speaking is tagged with their initials.
Mycroft is talking to you through Captcha./"Mycroft says..."Explanation Since Mycroft is, in essence, Big Brother, controlling all of the CCTV in London and generally running the world, it was decided on the Kink Meme that Mycroft was manipulating the LJ Captcha, used to filter out spambots
"Rupert Graves is good at football and has five children."Explanation On the commentary for "The Great Game", Benedict Cumberbatch is asked to describe why he likes Rupert Graves (Lestrade). He answers with that quote, in one of the campiest of all Camp Gay voices
"I'm not a psychopath, I'm a high-functioning sociopath. Do your research." Explanation Sherlock to Anderson, in response to being called a psychopath one too many times.
"Oh. God. Yes."Explanation John's rather Ho Yay-ish response to Sherlock asking if he wants to see some more death and danger. Used rather often in anonymous responses to Kink Meme prompts
I BELIEVE IN SHERLOCK/MORIARTY WAS REAL/SHERLOCK LIVES!Explanation at the end of The Reichenbach Fall, Moriarity sets things up to make Sherlock seem to be a fraud in the media. Several Sherlock fans have now started a 'campaign' stating they believe Sherlock's innocence
"Fine. It's...all...fine..."Explanation John is trying to learn whether Sherlock has a girlfriend or a boyfriend without sounding homophobic or...interested
Martin Freeman is a hedgehog.◊ Explanation Some cheeky Tumblr user compared Martin Freeman to a hedgehog. The meme exploded, with pictures like "yawning Martin/yawning hedgehog" and "grumpy Martin/grumpy hedgehog" spreading like wildfire. The capstone on the whole thing was Freeman's partner Amanda Abbington's Tweet response to a twitter user who asked if Martin knew about the meme and how he reacted, to which Abbington responded, "He laughs, he cries, then he curls up in a prickly little ball and hibernates for the winter." It also later spawned "otters who look like◊ Benedict Cumberbatch".
Certain photos of Moriarty are happening now too, with two of his more expressive faces from The Great Game. The first is an angry face with some kind of violent action as the caption, ex. "I WILL BURN-" and the second is a chill expression with something like "-you a CD of my favourite songs." Known as Misleading Moriarty.
"Fuck you, I won a BAFTA"Explanation Martin Freeman's snarky response to an interviewer teasing him about his character's lack of dialogue