'Minds Like Ours Dream Up' by BlackEyedGirl - John makes models, showing the heights of the buildings and the way Sherlock had been out of John’s sight for only a moment. Not long enough for a miracle. John/Sherlock (BBC tv series).
'He's Not Paid Enough to Deal with This Shit' by janonny - When John had found out that there was another Holmes running around London, he had been horrified. Bad enough that Mycroft was procreating, here was another full grown one carrying the same loopy genes. John was braced for all manner of strangeness. John/Sherlock (BBC tv series).
'Most Ghosts Are Idiots' by GoldenUsagi - on the lookout for suitable accommodation in London, John Watson finds himself renting an unexpectedly reasonably priced flat in Baker Street. The problem? There's already someone living there, if 'living' is the right word... Gen.
'Twisting and Turning the Colours in Rows' by leopardwrites - a nicely-written fusion with the book/movie Let the Right One In though you don't need to know the other source to appreciate this story. John is 13 and being bullied at school by the sadistic Moriarty and his clique, only for his life to be turned upside down in ways he couldn't possibly imagine by the arrival of a new neighbour. John/Sherlock (TV series).
The 'Compatible Damage' series by branwyn - two stories completed to date ('The Skeleton Winter' and 'Let Sense Be Dumb'), this is an outstanding genderswap AU series where John Watson is Joanna Watson, just as battered as the original and if anything outsiders seem to understand their relationship even less when Watson is a woman. Sherlock/John (tv series).
'In the Land of the Blind' by Tangles - Sherlock's been acting strangely for days. There's a claustrophobic silence to the flat, experiments tossed aside or abandoned, cases ignored. It's almost as if nothing matters any more. John's determined to know why. Sherlock/John (tv series).
If there's one cliche I really love, it's amnesia stories - here's a cracker in the Sherlock fandom, 'Lacuna' by coloredink. In which John has amnesia and can only remember waking up in his hospital bed, with nothing of what was to come after that, nothing in particular about his infuriating flatmate. Sherlock/John.
'Sic Gorgiamus Allos Subjectatos Nunc' by etothepii - a series of three stories (so far, I hope!) where John and Harry Watson are related to those famous Addams and are just as odd in their own way as the folks we've met from that family. It should probably be said that these stories are not for the squeamish... Gen.
'Secondary Exposure' by thesardine - as if John Watson's brush with death in Afghanistan wasn't enough to traumatise him, here the author also has him escaping from a serial killer when Watson was a teenager, a killer who seems to be continuing to prey on blond-haired boys. Heavily implied Sherlock/John.
'The Man By Any Other Name' by mia6363 - in an AU that takes some of its inspiration from the Bourne movies, John is a man without his memories fished out of the North Sea. Sherlock is himself, their paths colliding when John is involved in a robbery and Sherlock is asked to figure out who he might be. The truth, of course, turns out to be anything but simple. Sherlock/John (tv series).
As a follow-up to 'Ain't Seen the Sunshine (Since I Don't Know When)', which I recced in February, eleanork has also written another story in this universe (and hopefully more to come!) where Mycroft and Sherlock are children and Watson is their long-suffering but well-armed nanny: in 'Snowflakes (Like Dust in the Sun)' Sherlock disappears from school, causing all sorts of anxiety for everyone else. John/Lestrade.
'Constant Reminders' by irisbleufic - It was then he noticed that, if he were to make a job of it, he'd have his work cut out for him. Socks lurked everywhere in the room, it seemed: peeking out from beneath Sherlock's pillow, skulking along the lowest level of the bookshelf, and even cozying up to wantonly splayed book covers.. Sherlock/John.
The 'A Priori' universe by rubberbutton - starting with 'A Priori', and continued in two more stories to date, this is an AU where the world is run by vampires with humans as their slaves and Mycroft insists that his brother have a human slave despite how badly things went when he had a dog. Sherlock/John.