As You Are, by 13empress. Slash, Kirk/Spock. (ca. 10,700 words)
I don't often rec PWPs, but this one has a really cool perspective, in that it is alien-kink, but from Spock's POV, so the humans are the ones looked at through the xenobiology lense. The AU premise (though I guess it could converge with canon) is that before Spock attends Starfleet Academy he wants to have a human sexual experience, as he has heard all kinds of things about human sexuality. So he spends a day with rentboy!Kirk. It's not humor, but not extremely angsty either. (also on AO3)
This Place at the Crossroads, by alpha_hydra. Slash and het, Kirk/Spock, Scotty/Uhura. (ca. 33,600 words)
I loved the worldbuilding and AU scenario of this AU. The premise here is that humans weren't among the founders of the Federation, and Earth's warp capability delayed compared to canon, but that Starfleet eventually sends observers, because they are close and Earth is in a contested (with non-Federation) region.
Extra-curricular Activities and its sequel Academic Matters, by Amanda Warrington. Slash, Kirk/Spock. (both ca. 15,500 words)
In this AU Kirk and Spock meet and become a couple earlier at the Academy, and the sequel then explores how his academic hearing and the Nero events would play out. (also on the ksarchive)
A Little Left of Ordinary, by Anonymous. Slash, Kirk/Spock. WIP (ca. 6,300 words so far)
This one is a retelling of the movie in a vaguely steampunkish fantasy setting where magic also works. I really enjoy the worldbuilding so far.
Homo homini lupus, by Casspeach and Chaosraven. Slash, McCoy/Chekov. (ca. 13,600 words)
This is a Viking AU done as collaboration for the Trek Reverse Bang. The art was lovely, and Bones as somewhat reluctant Viking raider was great. (also on AO3, needs an account)
Of Sentinels and Anchors, by Corpus Invictus. Slash, Kirk/Spock. (ca. 13,000 words)
The premise of this one is that Sarek died when Spock was young, so Amanda raised him on Earth and he lacks Vulcan training. As a result Spock has also problems controlling his telepathy. I really liked the Spock-angst and h/c. If you mind the "special mental bond" trope you might want to skip, but in that case Kirk/Spock is probably not your pairing anyway. I however have a soft spot for the same.
Take Refuge in What You Know, by Corpus Invictus. Slash, Kirk/Spock. (ca. 120,300 words)
Kirk and Spock are neighbors, and Spock is agoraphobic. Which sounds like a weird premise, but I'm enjoying how their relationship develops here, and the story makes this work.
Nothing Lay Between, by Dancing Mercury and Jantra. Slash, Kirk/Spock, Pike/Spock. WIP (ca. 43,300 words so far)
Spock is given to Kirk by the Vulcans as a reward. The premise sounds as if it could only work if the setup is in alignment with your kinks, but this one actually has good worldbuilding, gradually gives background for the differences and isn't all that over the top when it comes to changing the characters.
Love is Strange by Garryowen. Slash, Kirk/Spock. (ca. 45,000 words)
I did not actually like Dirty Dancing as a movie, so I'm not sure why I really enjoyed the Star Trek version, or how it could even work with Spock and Kirk, but there you are, and it really does, and you should check this out. Whether or not you liked Dirty Dancing. (Also thinking about this, it is rather disconcerting to realize that I know people in fandom now plenty old enough to have been writing porn for some years, who weren't even alive back when that movie came out, and a ton of my classmates were crushing on Patrick Swayze, who is now dead. Memento Mori moments everywhere.) (also on AO3)
Knives in the Water, by green_postit and steam_pilot. Slash Kirk/McCoy. (ca. 18,500 words)
This is a collaboration done for the Trek Reverse Bang, and the art is very stylish, with a stark, noir-like atmosphere. The story is a gangster AU, and it had me really hooked, even though I'm normally not that into Star Trek AUs not somehow still set in space. It convinced me of them as mob for the duration of the story, and how Bones was drawn into this was great. Also, normally I don't emphasize warnings again in my recs that the header gives, but the warning for torture and abuse on the story is really not kidding, it was great, but brutal and intense. (also on AO3)
The Hounds of Morrigan, by Hounds_morrigan. Het and slash, Kirk/Spock/Uhura. (ca. 20,000 words)
In this AU Nero was smart enough to destroy Vulcan, Earth and the Federation right away rather than wait for Spock to be able to gloat. The resulting apocafic universe is not that close to canon, but who could resist Uhura, Kirk, and Spock ending up as badass and somewhat traumatized crazy space pirates? It has the additional benefit of working for my slavefic kink and some others. On the flipside, if you don't share my fondness for a variety of non-con and power inequality kinks, you might not enjoy this as much. (also on AO3)
all the lights that lead us there, by Irnan. Gen. (ca. 1,880 words)
This is a cool sentient!Enterprise story.
Like A Riot (Don't Need Order), by Jane Potter. Slash, mainly Kirk/Spock. (Some stories are finished, but the universe is still a WIP, ca. 120,000 words so far.)
In this AU Vulcan is isolationist, and Earth has an alliance with the Orions. Meanwhile Kirk, Spock & Co. set out to become space pirates. The universe is still a WIP and I like the first story more than some of the later parts, and some of the characterization (in particular of McCoy as this kind of alcoholic) doesn't really work for me, however this is still quite a lot of fun to read. (also on AO3)
Open Up My Eager Eyes, by June. Slash and femslash, Kirk/Spock, Uhura/Gaila. (ca. 15,000 words)
This is a fusion with Pump Up the Volume that was written for reel-startrek. I really enjoyed this, even though I'm not particularly into high school AUs or into making Spock a human/loosing the SF elements in Trek fiction. (Sadly, I don't have a working link to the story anymore, the journal where it was archived has gone f-locked.)
Aurora, by kianspo. Pre-slash, Kirk/Spock. WIP
A "Spock is raised on Earth with Kirk" AU, which is a trope I love, and so far this is done well. Unfortunately it hasn't been updated recently. (also on AO3)
Streetlight People, by ladyblahblah. Slash, Kirk/Spock. (ca. 54,400 words)
This has a great mix of angst and slowly developing friendship and romance. And I liked that this uses the prostitution trope without plodding the well worn "Pretty Woman" rescue/redemption path, even though Kirk eventually quits the (legal) sex work. (also on AO3)
Lensflare Lover, by Leftarrow. Het, Pike/Enterprise, Pike/Number One. (ca. 7,300 words)
This has a cool premise in which the spaceships have avatars. (Sadly, I don't have a working link to the story anymore, the journal where it was archived has gone f-locked.)
Walls Burning, Towers Turning, by Leftarrow. Slash, Kirk/Pike. (ca. 5,000 words)
This is a fantasy AU with really neat worldbuilding. (Sadly, I don't have a working link to the story anymore, the journal where it was archived has gone f-locked.)
Only Good for Legends, by Leupagus. Het and slash, Spock/Uhura and Kirk/Spock. (ca. 150,000 words)
This takes place in the Star Trek universe, but Spock has become a police detective on Earth rather than joining Starfleet. I'm enjoying the worldbuilding and the bits of character background that have been revealed so far to explain the changes. It has some angst (the whole cynical detective aspect and some of Spock's backstory) but is also quite lighthearted and funny without being crack or parody. (also on AO3)
Time's Divergence, by Logical_stimuli. Gen, Kirk, Spock Prime. (ca. 6,600 words)
This is domestic kidfic fluff that will make you feel warm and fuzzy: Spock comes through the wormhole at the same time as Nero, and because both of Kirk's parents are killed Spock raises Kirk.
In Truth, by Mint_amaretto. Slash and het, Kirk/McCoy, Spock/Uhura. (ca. 3,570 words)
This is a really creepy, twisted AU, as any mix with the Dollhouse concept (not the series itself, more the basic premise) should be.
Of Pilots And Groundbreaking Inventions, by Misfit_fandoms. Gen, Sulu (though the author labelled it as pre-Chekov/Sulu). (ca. 4,900 words) WIP?
The premise here is the Enterprise as a steampunk ship with an oddball crew. This feels more like a setup rather than an entire story, and the author said there might be more in this universe, but even as it is the atmosphere of this AU is neat and I enjoyed it as it is.
All the Past We Leave Behind, by Northatlantic. Slash and het, Kirk/McCoy, Spock/Uhura. (ca. 22,500 words)
This is a Western AU and still manages to transfer the characters and even the movie plot well.
Fighting Gravity, by Pantswarrior. Slash, Kirk/Spock. (ca. 138,700 words)
In this AU Spock doesn't join the Enterprise for its first mission. He and Kirk run into each other on earth afterwards, and this story slowly develops their relationship and reveals the backstory of what happened to Spock.
In Which We Change, by salvaged_pride. Slash, Kirk/McCoy. (ca. 14,160 words)
This is a AU with Kirk as werewolf, and I really like the werewolf premise here that the wolf is not aware of the human self, and how it was handled.
Twice Shy, by Sarka. Slash, Kirk/McCoy, implied Spock/Uhura. (ca. 20,000 words)
Bones is a werewolf, pining after Kirk. I never knew I wanted a Star Trek werewolf fic before reading this, but this was a fun scenario.
Emissary: The Illustrated Pilot, by Tassosss. Gen. (ca. 2,000 words)
This is a fusion with Farscape, and simply awesome, because the Enterprise as Leviathan and Spock as pilot make me happy.
Another Boy, Another Planet, by Vaingirlfic. Het, Kirk/Uhura, Spock/Uhura (with implied past Nero/Kirk non-con). (ca. 8,200 words)
This was posted to the het_idcrack challenge for a reason, so whether you'll like it probably depends on what your buttons are. However it pushed a lot of mine. In this AU newborn Kirk was captured and enslaved by Nero, and eventually during the events that parallel the movie Uhura rescues him. Her backstory is different as well, but I do not want to spoil it too much. (also on AO3)
The Will of the Force, by Verizonhorizon. Slash, Kirk/Spock. WIP
This is a fusion with Star Wars, with Vulcans as Jedi.
The Sky Was Made for Us Tonight, by Waketosleep. Slash, Kirk/Spock. (ca. 5,500 words)
In this AU Vulcans decided to supervise humanity more closely, and Kirk and Spock are delinquent rebels together after meeting in a holding cell and staging a prison break. I enjoyed this scenario a lot. (also on AO3 with a sequel)
An Illogically Beautiful Mind, by Waldorph. Slash, Kirk/Spock. (ca. 8,215 words)
This is a fusion with Good Will Hunting. (Now expanded into a longer series.)
Leave No Soul Behind, by Whochick. Slash, Kirk/Spock. (ca. 259,000 words)
This has Kirk, Spock and McCoy in Starfleet, but as part of some emergency service who rescue survivors of battles and the like. The worldbuilding and background for the characters is still becoming clearer as this progresses, but Vulcan was destroyed by the Narada in this universe as well. And there is plenty of action adventure mixed with personal angst. Anyway, it had me completely hooked.
Shadows of a Man, by Syredronning. Slash, Spock/McCoy. (ca. 32,000 words)
The basic premise is that Kirk and McCoy did not get rescued from Rura Penthe, and a war between Federation and Klingons followed. And this deals with the later aftermath for McCoy and Spock. On the one hand I don't want to spoil this, on the other hand the main reason I'm reccing this was that it did not go like I expected from the way the story seemed at first. In the end it left me somewhat sucker-punched, if in a good way. (I hope that was vague enough.) And on the whole it is quite a bit darker than what I usually rec (starting with that Kirk is dead from the outset, and character death is not my thing usually). However it is not completely bleak, and worth reading.