PART II CAN BE FOUND HERE.
i-knew-him-he-was-nice: Great question! There are so many amazing fics in the Sherlock fandom that it’ll be hard to narrow it down to just a few (and you’ll see from the list that I mostly failed at keeping it small), but based on what I’ve seen, here are some fics that are must-reads (since Sherlock/John fics are such a big part of the fandom, this list reflects that pairing, mostly, but I’ve added a section at the end for classics among other pairings as well):
Two Two One Bravo Baker by abundantlyqueer
Captain John Watson of 40 Commando, the Royal Marines, is assigned to protect and assist Sherlock Holmes as he investigates what appears to be a simple war atrocity in Afghanistan. An intense attraction ignites between the two men as they uncover a conspiracy that threatens everything they’ve ever known, but Sherlock is as much hunted as hunter, and everyone close to him is in deadly danger. Can he solve the case in time to save himself and John?
Alone on the Water by mad_lori
Sherlock Holmes never expected to live a long life, but he never imagined that it would end like this.
Given in Evidence by verityburns
Coming back from the dead can be a complicated business. With a new case on the horizon, rebuilding a life is one thing… rebuilding a friendship quite another. For Sherlock and John, things may never be just the same…
The Progress of Sherlock Holmes by ivyblossom
Sherlock is head over heels for John, but you wouldn’t know it by looking at him. First-person present-tense series of short scenes from Sherlock’s point of view, borrowing heavily from Arthur Conan Doyle’s stories.
A Cure for Boredom by emmagrant01
They’d never talked about sex in the year they’d known each other. Well, that wasn’t quite correct: Sherlock had never said a word about sex; John had bemoaned his personal dearth of it on many occasions.
But Love is a Voice on the Wind by Snow
From the prompt: Sherlock keeps getting texts from Mycroft with tips on wooing John.
"Take his arm. MH"/"Tell him about the sugar cubes. MH"/"Let him catch you looking once in a while. MH"
Sherlock resents this (I don’t need your HELP, Mycroft), but does them anyway.
Homemaking by rageprufrock
The original plan for returning to England involved fucking around being shellshocked and suffering mandatory post-combat counseling and physical therapy to dissect the shattered mosaic of his feelings. That’s not quite how it goes.
The Whore of Babylon was a Perfectly Nice Girl by out_there
Sherlock walks into a room and takes all the space right out of it. He does the same inside John’s head.
Performance in a Leading Role by mad_lori
Sherlock Holmes is an Oscar winner in the midst of a career slump. John Watson is an Everyman actor trapped in the rom-com ghetto. When they are cast as a gay couple in a new independent drama, will they surprise each other? Will their on-screen romance make its way into the real world?
The Quiet Man by ivyblossom
"Do you just carry on talking when I’m away?"
Stranger at the Gate by bendingsignpost
As far as initiation rites go, kidnapping a human doctor from a defended town ought to seem extreme. When James Moriarty offers him the challenge, Sherlock never considers saying no. (Fantasy vampire AU)
Observations on Sentinels and Guides in Victorian London by RyuuzaKochou
A Victorian era AU where Sentinels and Guides are members of everyday society. Starring Sentinel! Holmes and Guide! Watson.
The sensation of falling as you just hit sleep by greywash
Love is a much more vicious motivator.
Infiltrate (tear down the walls and the gate) by SkipandDi
This is a moment Sherlock will look back to time and again as the future stalks forward; an instance he will use to justify his actions, the decisions he will make. He’d known Moriarty was working solely for his attention, even John had recognized as much during the first assault. But Sherlock has been a fool, a dangerous, incompetent fool, because this is so far beyond all that. It always has been.
Cowritten with MirrorSkippy.
26 Pieces by lanning
Mycroft gives Sherlock the apparently simple task of solving a puzzle box containing a stolen microchip. It isn’t simple.
A Study in Winning by Jupiter_Ash
John and Sherlock are professional tennis players and it’s Wimbledon. One is a broken almost was at the end of his career, the other an arrogant rising star tipped for greatness. It should have been a straightforward tournament. It really should have been. How were they to know that a chance encounter would change everything?
Equilibrium by augustbird
At Baskerville, John is infected by a virus that turns him into a genius. But when the infection progresses into neurodegeneration, it’s a race against time to save himself. Flowers for Algernon fusion.
The Real Meaning of Idioms by feverishsea
After two weeks away, John finally texts Sherlock. He doesn’t expect Sherlock to respond. He doesn’t expect Sherlock to keep texting him. And he really doesn’t expect things to spiral out of control so rapidly.
A Priori by rubberbutton
In which vampires have enslaved humans and control, well, everything. Vampire!Mycroft insists his little brother get a slave — even though it didn’t work out with the dog — and Sherlock chooses the one guaranteed to irritate his brother the most: an unassuming little doctor with an ugly past and absolutely no style to speak of.
Baker Street Series by magicbunni (suggested by Anonymous)
Conspiracy and murder find Sherlock Holmes and John Watson surrounded by covert enemies in the heart of Scotland Yard. Together, they unearth clues that illuminate the scope, depth, and distorted psychology behind the crime. And, after a pre-emptive strike ordered by the mastermind they pursue, Holmes elects to continue the investigation under conditions that will force John Watson to fight for his friend’s — colleague’s — life.
Paradox series by wordstrings (suggested by Anonymous)
In which what’s in Sherlock’s head is never going to get any better, and John is nearly thrown out of his flat.
The Heart in the Whole by verityburns (suggested by silverseamstress)
Events after ‘The Great Game’ leave Sherlock dependent on his best friend and colleague. But John has a secret of his own…
Winter’s Child by Canon_is_Relative and ImpishTubist (suggested by silverseamstress)
Five years after they meet, John and Sherlock adopt a baby boy.
At Least There’s the Football by sheffiesharpe
Lestrade arrives at the pool after the explosion and finds someone else is already there.
Give Me A Label (I’ll Make Confetti) by IBegToDreamAndDiffer
Gregory Lestrade is the local badboy. He drinks, he smokes, he has sex, but that’s what a lot of seventeen-year-old boys do. Not Mycroft Holmes, of course; that posh git wouldn’t know what to do with a bloke. That’s what Greg thinks until he sees a new side of Mycroft, and every label he’s ever used is torn down in seconds.
The Making Of by emmagrant01
In the aftermath of Sherlock’s death, John Watson and Greg Lestrade take comfort in each other. But of course, Sherlock isn’t really dead, so this is all about to get complicated.
Stolen by fireofangels
Kidnapped by Moriarty, Sherlock is gradually made into Dark!John’s good little girl, while everyone else thinks he is dead. Will he be saved in time?
Please be aware that this fic plays with chronology and dream states and is deliberately hazy and confusing.
The Physics of Present Tense by paxlux
It happens instantaneously, but it takes years. It’s like looking up at the stars and spinning around with your arms out and letting gravity take you.
The Fine Art of Distraction by Sapphy
Sherlock has always been a little more fascinated with murder than is strictly healthy, but he’s staying firmly on the right side of the law. With a little help from his friends.
Sustain (or Concerto for the Famished in D Minor) by maybe_amanda
"So now you’re behaving like a six year old ‘cause he didn’t take you along on his honeymoon?" Lestrade said. "Grow the hell up."
As a final note, one thing you should definitely do is check on Archive of Our Own, the site that hosts a lot of Sherlock fanfiction, and filter by the ship/rating you want (or leave it free for all fics from any category), then sort by hits. That’ll show you the most widely read fics, which are the likeliest to be the “classics” of the fandom. A lot of those are probably covered here, but you might find some more as well. Hope that helped!