Be warned: Most of these are on the KinkMeme.
The Prince of Aquitaine Before His Ruined Tower Selkie!John. He puts on his skin and leaves. Sherlock returns to find no sign of John and sets out on an epic quest to find his friend.
First Time Smut with Manipulation NC-17 John thinks Sherlock is a virgin. Sherlock plays along.
A Study in Magic John is a Wizard.
Moving in a Still Frame John bursts into Scotland Yard one day, emotionally unstable and shouting, "Tell me the Statute for Sexual Assualt or do I have to go out and kill somebody?" Everyone thinks John was raped in Afganistan, but it's Sherlock who is in trouble.
An Equal Partnership It's hard to be in a relationship with someone who can tell all your deepest darkest decrets at a glance. Sherlock tells John his own secrets to convince him to stay.
Poco Agitato John and Sherlock begin to tire of sex. They wish for a bit of rough play. BDSM style.
Werewolf!John wants you away from his Sherlock John gets bitten by a werewolf and it slowly starts to change his demeanor. He begins to see Sherlock as his mate and becomes very VERY possessive.
If Only John has a nightmare. Sherlock sings him to sleep.
Fuck or Die John is forced to rape Virgin!Sherlock
Doctors really do make the worst patients John/Joan gets injured and calls for help. Mycroft/Sherlock and Lestrade makes her regret calling people who would make sure she HAS to be checked over.
Not what it Means Sherlock and John get into an argument. John walks out after calling Sherlock a freak.
Kidnapping Mycroft kidnaps John so regularly, he can predict when it happens. Things get interesting when John replies absently, "Oh, no. Can't. I'm getting kidnapped then."