Okay I'm going over my history of fics read on my AO3 account so I thought I'd pop a few recs in for you all...
Skeleton Key
Sherlock Holmes is anything but predictable; a fact that John has grown used to over the year they have known each other. However, nothing could prepare him for his reaction to Sherlock's mysterious decision to pierce his tongue. (Eventual John/Sherlock)
Ten Days
Warnings: This one is extremely dark for John - includes rape and torture.
Sherlock Holmes has been dead for forty months, and John is at last beginning to live his life again. But just when he is beginning to believe that he might be happy, his world crashes back down around him.
John is named a missing person. Someone is pointing DI Lestrade in the wrong direction. And as the days pass, his situation only grows more dire. It seems like the disappearance of his best friend is the only thing that can bring Sherlock Holmes back from the dead.
We Go Anywhere But To The Ground
Warnings: Post TRF; Suicidal Ideation; Suicide Attempt
Every second that ticks by is a reminder of the deafening quiet Sherlock has left behind. John feels his soul slip out of his fingertips, inch by inch, with every passing day.
At some point, he stops trying to hold on.
And Stand There At The Edge of My Affection
"You've written love letters," Sherlock asserted.
This one is a cute little one-shot where Sherlock seeks John's advice on how to write a love letter.
The Sign of the Four
A year and a half post-Reichenbach, a damaged Sherlock Holmes returns to Baker Street. But everything's changed, leaving the friendship between Sherlock and John tense and uncertain.
While struggling to adjust, Sherlock, John, and Mary Morstan find themselves on a case involving betrayal, deception, and tests of friendship. But will it make their bonds stronger or tear them apart? And will it matter if Sherlock's demons pull him under first? An incredibly angst-filled adaptation of the Sir Arthur Conan Doyle novel. Essentially designed as a theoretical 'next episode' of the show.
I read this one ages ago but I think I ended up reading it twice. I enjoye it but I couldn't tell ou why now 
The Best of TImes
Struggling to cope with life after Reichenbach, John is gravely injured during a vicious, apparently motiveless street attack. Convalescing, on Mycroft’s invitation, at the Holmes family seat, John encounters someone entirely unexpected and uncovers an intriguing seventeen year-old mystery. Things hot up as John finds himself battling to work out the solution before James Moriarty’s legacy catches up with him – and also rekindling a love affair that was never really given the chance to blossom.
This one is a bit of a mind-feck; unanticipated (well, partially anticipated if I'm being honest) twist.
Filthy/Gorgeous
Even if this was legal, even if there was nothing technically wrong with what he was doing he knew that if he were caught, or if he were seen by someone he knew, or if he were found out in any way the shame would never, ever die. What would his regiment say? What would his family say? What would anyone say if they discovered that John was currently in a cab on the way to pick up a male prostitute for the evening?
This one is a WIP; AU; not 100% sure about it yet given the whole WIP-status but it's fairly well written.
Okay - I think that'll do you for now 
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I dislike being outnumbered. It makes for too much stupid in the room