I would say "a surprising number of OT3 stories" but honestly it's not surprising.
Community
Astraphobia by wiltedviolets
(complete)
Abed and Troy, it turns out, are both afraid of thunderstorms. Annie knows this because at one-thirty in the morning, long after any reasonable person should be in bed, someone starts pounding frantically on her door.
Citizens of Amity by thingswithwings
(complete)
Includes many hugs. [Abed/Troy]
Introduction to Friendship Reciprocation by Miazaki
(complete)
It's not only Troy who's patient with Abed. Theirs is a friendship that goes both ways. [Abed/Troy]
Homestuck
hey there bright-eyed mister melancholy by attentionmerrymakers
(complete)
This is why you are sitting in Can Town making your fifty-sixth scale replica of a sheep. [Dave/Karkat]
plie, ma fille, ne te brise pas (mother loves you) by kyhc
(complete)
You give her a name that means frightening, and it fits just so because you're terrified of raising her wrong. [Lalonde Family]
Leverage
[Alec/Eliot/Parker]
The 40mg Job by norah
(complete)
Parker takes the Second Act Rehabilitation Center therapist's advice seriously.
Come Closing In For A Kill by egelantier
(series) [Fantasy Royalty AU]
On the day King and Queen leave, Her ex-Majesty looks at him and says with a surety of knowing her answer: "Promise me you'll keep them safe." Eliot says, "Until my dying day," and knows it to be the easiest truth he ever told.
like you know I am better than the worst thing I ever did by postcardmystery
(complete)
"Yes," she says, "And how long have you known that?"
Roosterteeth
Blue by MdeCarabas
(complete)
Four months after getting captured by Locus, Washington finally gets rescued. [Red vs Blue | Tucker/Washington]
Embers by bellmare
(complete)
Some people just want to watch the world burn. [RWBY | Ruby/Weiss]
Reintegration by Nemonus
(complete)
"So, if I'm the Alpha - which I am still not sure about, by the way - shouldn't I have some sort of magic ghost power over the other AI?"
"They want you," Wash said. "That doesn't necessarily mean that you have any power." [Red vs Blue]
Shingeki no Kyojin
inseparable by kiteflower
(complete)
but seemingly unreachable. [Armin/Eren/Mikasa]
Of Girls and Monsters by Jelly
(complete)
It's been years since those days, but she still doesn't know if she's a girl that can become a titan, or a titan disguised as a girl. It matters though, because he treats her as a human being, and it feels like forever since someone saw her as anything other than a weapon. [Annie/Eren]
we will die with out arms unbound by attentionmerrymakers
(complete)
Tonight she keeps a close eye on him. His face is bright with a harsh kind of mania.
"Go to sleep, Eren," she says, after a while. There are smears of sleepless black beneath his eyes. He shakes his head, a book in his hands. [Armin/Eren/Mikasa]
Misc
An Answering Ripple by Mellacita
(complete)
Unbidden, an image comes to his mind. A tall figure, dark-headed, lonely, standing on the shore as all of time swirls around him, casting his love into a lake and watching for answering ripples that never come. [Merlin | Arthur/Merlin]
At the Join by entanglednow
(complete)
Tony's gone down on one knee, fussing with one of the heavy-duty boots, and Steve's going to say something. But there are already knuckles smacking the side of his leg, and he's lifting it without thinking. [Avengers | Steve/Tony]
falter and fall by Aoida_blue
(complete)
Jason doesn't think, Kori and Roy don't falter. [Red Hood and the Outlaws | Jason/Kori/Roy]
Lotus by gladdecease
(complete)
While studying the basics from Mei at the school where she learned alkahestry, Al comes across a wall hanging with an interesting, familiar subject. [Fullmetal Alchemis | Alphonse/Mei]
Planet Megalodon Wraith Defense Force by pentapus
(complete)
John was just going to have to accept that his dignity was a necessary sacrifice for Rodney's peace of mind. Or: the one with the sharks. [Stargate: Atlantis]
this love was not your trainwreck by postcardmystery
(complete)
Pretend that you made up the vampires, and that this is all that there is. [Being Human | Alex/Hal/Tom]
Trying Promises by gladdecease
(complete)
Of course Lee would try to befriend a ninja who'd nearly killed him once; that was practically his modus operandi. [Naruto]
vox populi by bellmare
(complete)
You have never believed in heroes. [Gatchaman Crowds | Hajime/Rui/Sugane]
we walked this line with dust in our pockets by timewaslost
(complete) [Modern AU]
She's twenty-five and she says find him. [Once Upon a Time | Aurora/Phillip/Mulan]