The end tag of "Advanced Criminal Law" features them playing the rather suggestive game of "How many pencils can I fit in the other's mouth?" complete with mischievous expressions and a bit of gagging. Troy won.
The 'Somewhere Out There' duet.
From "Politics of Human Sexuality"... Troy, on playing basketball with Abed: "It's impossible to guard you — your eyes are too gentle and mysterious."
From "Romantic Expressionism":
Annie: "Troy... the other day, after Spanish, I thought he was trying to hold my hand, but... he'd just mistaken me for Abed."
Troy describing Abed as his other half.
"They're just jealous."
It's heavily implied in their Kickpuncher tag that they've recreated at least one sex scene together.
In Physical Education, after Abed says, "Truth is, lots of girls like me, because, let's face it, I'm pretty adorable," Troy can be seen nodding in affirmation.
Their "Awesome Elevator" routine, in which they sink down to the ground and very quickly switch shirts before rising back up again. Troy follows it up with a somewhat suggestive "That was awesome."
The end tag of Modern Warfare has Troy obsessively re-recording a voice message for Abed... about meeting up with him in ten minutes. His level of fretting is not unlike that of a dedicated significant other, and this is acknowledged by Jeff as he cuts in to get the recording process over with.
Jeff: Hey Abed. Your girlfriend will meet you at the flagpole in ten minutes. Goodbye.
In "Epidemiology," Troy is shunned by a group of girls who are put off by his and Abed's excessively nerdy Halloween costumes, and realizes how far he has fallen from his Jerk Jock days in high school. Blaming Abed for his loss of social status, he changes into a "sexy" costume and proceeds to treat Abed as an embarrassment and liability... however, shortly afterward the party is overcome by a zombie epidemic with Troy and Abed as the last people standing. They end up trapped in the corner of an Abandoned Warehouse with a window allowing only one person to escape. Abed sacrifices himself in order to get Troy through the window, and in the last moments before Abed is overcome by the zombies, Troy looks back and says "I love you"... to which Abed responds with the classic "I know" from Star Wars. The whole moment is incredibly romantic and drips Anguished Declaration of Love, especially considering the fact that Troy has no apparent reference in mind when he chooses to tell Abed that he loves him. In fact, Abed turning the moment into a reference is the only thing keeping the scene from being viewed as a legitimate confession on Troy's part. Of course, neither of them remember it afterward, but the point still stands.
Also, once Troy runs back into the building to adjust the thermostat, he comes across his zombiefied friends. He has absolutely no problem making wisecracks and punching Annie, shoving Pierce and only pauses before Shirley because he can't reference something if he doesn't know what she's dressed at, but it's at this moment that zombie!Abed shows up. Cue Troy desperately trying to snap Abed out of it, complete with ABBA. The whole moment seems even more romantic given that the last thing Troy said to Abed was a love confession.
It's also not a desperate attempt to save his life, as he could very easily punch Abed and continue onwards: Shirley didn't actually have a hold of Troy, and it wasn't until after he was bit that the others did grab hold. Troy couldn't hit Abed, even at the risk of his life and, given Troy's knowledge of film, he had to know that trying to reason with a zombie never has good results.
Everything to do with Abed in "Advanced Dungeons and Dragons". Aside from his flirting with Jeff and implications that his character wants to have sex with Jeff's... he ultimately has sex with Annie's character, while she plays an attractive man called "Hector the Well-Endowed", which Abed wrote for Troy.
After Troy and Abed spend almost the entirety of 'Early 21st Century Romanticism' competing over a girl (in a way that they specifically designed to be a civil as possible so that neither would compromise the other's feelings), she eventually chooses Troy. Troy's almost immediate reaction is to ask her what she didn't like about Abed, becoming defensive when she implies that he was not a romantic option because he's "weird", and storming out to rejoin Abed and have a heartfelt conversation with him.
Troy: There's someone out there for us.
Abed: Happy Valentine's Day.
Troy: It is now. (They hug, and the aforementioned girl walks past, giving them a strange look.) Ignore her.
The end tag in "Critical Film Studies" opens on Troy and Abed finishing up a candle-lit dinner at a fancy restaurant, and when the check arrives, Troy insists on treating Abed to the meal (and flashes him a smile). The bill of course ends up being too much for either of their wallets to handle and they end up dining and dashing, but even so, there are few conclusions that can be drawn from those first few seconds other than "they were on a date."
It begs the question if Jeff and Abed's dinner was also a date. Troy was jealous throughout the episode, and it can easily be assumed Abed went out with Troy to make up for it.
In 'Biology 101' Troy and Abed officially state that they "have an announcement to make..." (cue uncertain looks from the rest of the group) ...they're moving in together. Later, we discover that they name their apartment Chez Trobed. Seriously.
Troy: Speaking of figuring things out, me and Abed have an announcement (They both stare at each other, smiling, whilst the rest of the group watches uncertainly).
Abed: Troy and I are living together.
After Shirley's pies burn in her timeline in Remedial Chaos Theory, she accuses the rest of the group of being "horny toads who sit around all night just making googly eyes at each other". This prompts the rest of the group to give each other significant looks, the combinations of characters consisting of Annie and Jeff, Jeff and Britta, Britta and Troy, and Troy and Abed (complete with suggestive eyebrows on Abed's part). Also worth mentioning is the fact that apart from the latter, all of these pairings have definitively been canon at some point.
In "Horror Fiction in Seven Spooky Steps," the study group is telling scary stories. Britta's, Abed's, and Annie's stories all feature two main characters who are involved in some sort of romance. The next story is Troy's, which opens with... he and Abed as Top Gun fighter pilots. Troy is carrying an injured Abed bridal-style through the door of a cabin. Then Pierce (a "crazy, old, racist doctor") drugs them, and they wake up under a blanket together on an operating table. Pierce pulls the blanket off and reveals that he's sewn them together. They proceed to look at each other and yell "FORCED TO BE TOGETHER FOREVER!" ...a situation they appear more than content with.
What amps up the homoeroticism even more is the fact that in the purple prose romance story right before Troy's, Jeff bridal-carries Annie in the same way that Troy carries Abed in his story.
The entire "Contemporary Impressionists"/"Digital Exploration of Interior Design"/"Pillows and Blankets" story arc. After Troy's sincere and loving defense of Abed's Cloudcuckoolander status to the rest of the group, Troy and Abed get in what is implied to be their first real argument (after Abed's childishness and irresponsibility crosses a line Troy isn't willing to support), and the storyline is played like a rift in a romantic relationship. This spills over into the rest of their interactions, until everyone from creepy air-conditioning-repair magnates to evil goatee'd alternate versions of themselves are telling Troy and Abed to split up. This leads to a small disagreement over pillows and blankets (or rather, forts made out them) blowing up into a major fight that causes them to sever ties with one another, only coming in contact in order to take out their hurt feelings on each other in the most dramatic and damaging way possible. Eventually, they are forced to acknowledge that they like each other so much that they are drawing out their "breakup" in order to delay the actual moment of separation, and begin to repair their friendship from the ground up. This is one of the most heavy, angsty, and character-driven arcs of the season, and is played to display the full depth and impact of Abed and Troy's relationship.
"Virtual System Analysis" really drives this home. For the sake of context: the last time one of Abed's emotional nosedives pulled the show into genre-bending surrealism, the event was triggered by his mother's abandonment. This time, it's Troy spending time with someone else, which puts a pretty intense spin on exactly how dependent Abed is on Troy for even a relatively stable emotional life. Doubles as both Fridge Logic and Tear Jerker.
The same episode gives us Abed (rather pettily, for him), "simulating" Britta and Troy's date and deliberately portraying Britta as an insufferable jerk, while Troy wistfully daydreams about "going home to Abed". Meanwhile, the real Troy takes time out of lunch to call Annie and make sure that Abed is doing okay. Seriously, the two of them might as well be telepathic and sewn together.
So, so much in "Curriculum Unavailable". According to Troy, Abed's usual demeanor is "adorable weird." Troy attempts to convince the therapist that his and Abed's adventures are "very manly"... while attempting to cuddle with Abed on the couch. He then remembers himself and offers Abed a hasty handshake. A flashback shows both Troy and Annie attempting to comfort a distraught Abed during the Daylight Saving's time-switch with hugs and caresses... also, when faced with the prospect of Abed being committed to an institution, Troy tearfully breaks down and begs the psychiatrist not to take Abed away.
In "Digital Estate Planning," Abed's avatar decides to abandon the study group partway through a computer game in order to stay with a female character and help her rebuild her life after Shirley and Annie murder her parents and burn down her house. Later, the group meets up with Abed again, and he informs them that his "wife" can make babies for him. Troy jealously retorts "Oh, and I can't?"... only to seem upset when he realizeshe can't.
"The First Chang Dynasty": Troy has been claimed by the air-conditioning repair school, and is told to give a final goodbye to his friends. He says a quick farewell to everybody in the group (including Britta, with whom the writers had been ship teasing Troy for several episodes)... and then, upon coming to Abed, leans in and whispers something inaudible in his ear. Abed later claims that he said "I know you hate when people do this in movies", but the moment is still rather ambiguous.
Considering how Abed couches everything in pop culture, that expression was probably genuinely intimate. The whole scene was constructed on heartfelt final goodbyes where the actual words were pointedly undramatic ("Never wear a rubber." "Never listen to Pierce.") but still anchored on characterization.
"Introduction to Finality": Abed practically experiences a months-long mental breakdown ( culminating in his temporary transformation into Evil!Abed ) after Troy's departure for the air-conditioning repair school; Troy also spends his months away pining for Abed. When Troy finally leaves the AC annex and is reunited with his friends for the first time, he comes upon Abed and Britta hugging, and asks "Can I cut in?"... only to completely ignore Britta's offered hug and embrace Abed.
In the season 4 episode, "Paranormal Parentage", Jeff refers to Abed as "[Britta]'s boyfriend's boyfriend" when he and Troy show up wearing matching costumes.
In the same season, Abed is again called Troy's boyfriend in "Conventions of Space and Time" (by Britta) and "Basic Human Anatomy" (Jeff again). The writers may have felt this was now safe to do as a joke now since Troy is in a heterosexual relationship.
The third episode of the fourth season is a giant ode to the Ho Yay between Troy and Abed. To keep it short, Troy feels replaced and goes "all psycho girlfriend" on Abed (Britta's words). It keeps going from there.
The show has gradually tended to deconstruct the Ho Yay between Troy and Abed in later episodes, however, pointing out that their relationship frequently tends to cross the line from "homoerotic best buddies" to "worryingly co-dependent on each other".
As befitting Troy's final episode, Geothermal Escapism demonstrates just how much Abed really cares for Troy. He constructed an entire game of 'The Floor is Made of Lava' just so everyone can see the world as he currently does. Abed equates Troy leaving with death.
Abed: By the way, when I cloned you, I had to patch the missing parts of your DNA with genes from a homing pigeon. You may notice side effects, like a compulsion to come back.
Community: The Dean and everybody. Especially Jeff.
Abed is a bit of a Ho Yay magnet. In the fried chicken mafia episode, Abed seems to have seduced Shirley's dread-lock guy away from her. In "Mixology Certification" Abed spends almost the entire evening being hit on by a gay man at a bar.
In addition to that, in "Critical Film Studies", Jeff and Abed have a fancy, candlelit dinner complete with "real" conversation because Abed noticed that Jeff was avoiding him. Jeff proceeds to have a more intimate conversation with Abed than anyone else in the group.
The episode "Physical Education" has a scene where Jeff has a pool match with his new billiards instructor. It features both of them getting naked and the instructor walking up to Jeff while both are still naked and then kissing him on the lips.
In the same episode, The Dean checking out Jeff's ass as he strips to his underwear and then carefully filming Jeff's naked pool match and going to give Jeff a congratulatory hug but stopping when he notices that he's sweaty.
We also have the dream sequence where Britta and Annie are in very short Cheerleader uniforms and push each other into a pool of bubbly water.
And the episode where they get in an oily wrestling match on the quad with guys throwing money at them, which actually happened.
And in the episode "Romantic Expressionism" the group discusses inter group romance, which leads to everybody looking at everybody else. Most notably Britta and Annie stare at each other for a few seconds as if they are contemplating a relationship. Annie gives a cute smile, and they quickly turn away from each other. Played for Laughs of course.
Annie tries to kiss Britta in one episode simply because a random member of the crowd yelled out for them to kiss.
In the above-mentioned scene where Jeff notes that there's nothing stopping any of the study group members of thinking of each other as a sexual prospect, there's also a glance between Jeff and Abed, ending in Abed giving a suggestive eyebrow wiggle.
Abed traded Britta's Spanish lesson card to Jeff in exchange for his shirt. "You don't understand. I want to wear it out of here."
Jeff also called Abed "Rakishly good looking" in one episode, they had the scene eating chicken fingers on the table like in "Sixteen Candles", as well as the My Dinner with Andre episode, Abed's hero worship of Jeff as Hawkeye, and the episode when Jeff moved in with Abed. Jeff and Abed were just as bad as Troy and Abed in early episodes
In Season 4, when Jeff mentioned "Settling arguments over who misses me most" Abed raises his hand
Chang gets touchy-feely with Jeff in the first season. "Let me rest gently on your pecs!" It's Played for Laughs and Chang is always creepy, but here he seems to be genuinely rebounding on Jeff, to the extent that Jeff goes to the trouble of getting him back together with Alessandra.
Britta made out with another straight girl because both of them thought the other was a lesbian and wanted to pretentiously stand up for LGBT rights.