In "Basic Genealogy" when Pierce hugs Jeff and comforts him after he starts sobbing and finally admits, after denying it for the entire episode, how upset he is about his break up with Professor Slater.
In the same episode, Jeff telling Pierce after his ex-stepdaughter Amber screwed him over, "If you have friends, you have family."
Jeff changing "Hot Blonde Spanish Class" to "Britta" on his contacts list.
Troy's speech about Annie after the bar in "Mixology Certification".
Jeff telling Troy, "You're a man, now." after Troy sacrifices his first drink to bring the gang home, also in "Mixology Certification".
When Pierce helps Annie with the rent in "Celebrity Pharmacology 212", and then they hug.
The end of "Abed's Uncontrollable Christmas," with everyone snapping Abed out of his Heroic BSOD with a song about how the meaning of Christmas can be anything good, followed by him saying they're his new family.
The gang steals the Christmas tree from the cafeteria, Shirley goes back to snag the menorah as well, in a touching turnaround from the year before.
Shirley's ex-husband/current boyfriend admitting all the drama is his fault, and going back to see the group. Their reactions are perfect.
The end of Early 21st Century Romanticism
Pierce pretends he's dying to Mind Screw everyone with things he's bequeathing to them...except Annie, who just gets a fancy tiara. She keeps trying to figure out what the catch is, but it turns out the gift was completely on the level, as she's Pierce's favorite.
Abed saving Jeff's Pulp Fiction themed party, even turning the surprise around on Jeff.
The conversation the two have before this as well probably counts, particularly when Abed reveals why he chose My Dinner with Andre as his movie 'homage', and Jeff's reaction to this.
Abed: It's a movie about a guy who has an unexpectedly enjoyable evening with a weird friend he's been avoiding lately. Jeff: You think I've been avoiding you? Abed: You and I did hang out more last year. It makes sense; everyone else is growing and changing all the time and that's not really my jam. I'm more of a fast-blinking, stoic, removed, uncomfortably self-aware type. Like Data. Or Johnny-5. Or Mork. Or HAL. Or KITT, or K-9, or Woodstock and / or Snoopy. Of courseSpockprobably goes without saying...
Jeff: Abed, I don't need you to grow or change. And take it from someone who just had a meaningless one; sometimes emotional breakthroughs are overrated.
After "saving" Pierce from a scam marriage, Jeff realizes his selfish reasons for doing so, and that the two of them really are perfect for each other, so he convinces the woman to go out on a real date with Pierce.
Britta and Jeff cooing over how cute baby Ben is before they realize that isn't cool.
Jeff to Annie: "You're a good kid, and I'd like to do my part to help you stay that way."
Abed and Shirley's "You humble me, you humble me, too" exchange at the end of Messianic Myths and Ancient Peoples.
Pierce inserting a certain lyric into the school song "Annie believes in me"
Pierce's mother's recorded message explaining how life is a beautiful thing, and that while death may be sad, it is simple a part of life that can't be avoided, nor should it be.
"I'll play myself out." (gangsta rap)
Britta's pep talk to Annie in "Football, Feminism and You", after Annie confesses her feelings for Troy in the Wondrous Ladies' Room:
Annie: I've been... infatuated with Troy. Now he's joining football. Now he'll have his pick of the litter... [Crying] and I'll never get to be with him! Britta: Oh, Annie, screw him! There are guys out there that would kill to be with you. And if Troy's not one of them, that's him failing your standards.
The group gets an entire one in "Advanced Dungeons and Dragons". The fact they would stage all of that for a person they didn't know very well is very sweet if you think about it.
Even better is how much Fat Neil's life ended up improving because of it. He went from a lonely, near-suicidal kid to the host of his own campus radio show, the guy in charge of the school's keys, and is dating Vicki to boot. The group really turned his life around.
Pierce lying that he bribed the biology teacher to kick Jeff out, sacrificing his newfound acceptance so Jeff can get back in the group. Jeff promptly realizes it, and also moves to keep Pierce in the group.
The end of Timeline "Prime" where Jeff gets the pizza and the group is dancing to "Roxanne" by The Police.
During the Gay Bash, where Pierce is dancing. He just looks so happy, which makes it sad when his father shows up.
Troy and Abed giving Annie their bedroom.
Their puppet show about Annie moving in with them.
And the puppet show with Annie as Princess Annie.
Jeff: I liked Horsebot-3000.
Britta calling out the Dean for being a tyrant after he fires Jeff from the commercial and leaving him crying. Showing that even with all the Dean's prima donna behavior as director, hurting Jeff like that had crossed the line for her.
The study group forgiving the Dean and Jeff initiating a group hug with him.
Abed decides to stop observing and start interacting for long enough to edit the commercial for the Dean after his breakdown and therefore save him from getting fired.
Luis Guzman's defense of the school and his assertion that he really enjoyed his time there. It takes on several layers considering that in-universe he's probably one of the school's most high-profile alumni.
Jeff and Shirley bonding over foosball and getting over their past as the victim and bully when they were children and walking away together arm in arm to watch a movie.
Also in that episode, how worried Annie was over breaking Abed's DVD. For a lot of characters, they would at the very least take a moment to question how it wouldn't be that bad an act. But even if she didn't take the case itself seriously, she knew the DVD was important to Abed and that was all that mattered.
After getting the study group involved with the Greendale Christmas pageant arranged by deranged Glee club director, Abed admits he just wanted everybody to spend time together, since they were all planning to do separate things for the holidays. On Christmas while watching the Inspector Spacetime Holiday Special alone in his apartment, Abed opens the door to find the group came to watch the special with him.
When Mr. Rad is yelling at Britta after her poor performance in the Christmas pageant, the way Jeff and Troy immediately snap out of their glee-club cheer and confront him after he calls her "the worst".
Jeff: "Hey!" Troy: "You do NOT get to call Britta the worst!" audience full of Greendale students: "Yeah!"
Also the fact that the rest of club, the audience and the Dean were perfectly fine with letting Britta sing her song, even if it wasn't very good.
Of all things, the line "For GCTV, this is Abed Nadir saying: did you know you can make napalm our of common dish soap and cat food?" can count as this. Of course, it's not so much what he says as why he says it.
Meta-example; in a roundtable interview with the female leads of the show and the head female writer during the 2011-2012 hiatus, towards the end when the show's uncertain future is being discussed Gillian Jacobs (Britta) becomes so heartfelt about how much working on the show and the friendships she's made while doing so have meant to her that she starts crying, and ends up needing to be consoled by her fellow actors. And then Alison Brie (Annie) joins in a few moments later.
The ending of "Pillows and Blankets". Jeff offers to collect the imaginary 'friendship hats' he (sarcastically) offered to Troy and Abed earlier from the Dean's office, and leaves the room to do so. Annie, like the audience, assumes he merely stepped out long enough to give the impression of going to the Dean's office, but is still touched that he engaged with Abed and Troy on their wavelength in order to help resolve their conflict. But then it reaches a whole new level when Jeff reveals that even though he knew perfectly well that they were made-up, despite himself he still went back to the Dean's office to get the 'proper' hats anyway, since helping Troy and Abed restore their friendship meant that much to him. He even 'fixes' them up from where they were dropped.
Initially, Jeff's dismissive of the whole conflict, manipulating each side so that he has a reason to avoid class. When he learns that it's escalated to the point where Troy and Abed are hurting each other's feelings, however, he immediately starts taking it more seriously and genuinely working to try and resolve it.
The end of "Origins of Vampire Mythology", which involves one of the sweetest unspoken exchanges in the show, if not the the sweetest.
The moment in "Curriculum Unavailable" where the study group realize that Abed's right and the Dean's been replaced... because the Dean clearly adores them too much to ever stab them in the back the way they think he did. And when they realize he's been kidnapped and replaced, they immediately resolve to rescue him.
The end of "Digital Estate Planning": after Gilbert is crushed by his father only letting him have his inheritance if he never reveals his parentage, the whole group forfeits the game so he'll get it by default.
Pierce and Gilbert bonding at the end over both their newfound relationship with each other and their absolute bastard of a father. Pierce seems genuinely and honestly thrilled by this.
Also the way the study group helped Pierce try to win his inheritance. They don't even think for a moment of taking it for themselves. Keep in mind that this is a group of unemployed adults who just got expelled from college.
The end of "Introduction to Finality": Darkness makes one more massive attempt to encroach on the study group's lives and fails horribly.Abed becomes self-aware enough to seek help and convinces Britta she's a good enough psychologist to give it to him, Troy talks the AC Repair School down from its crazy and gets it to let him lead a more well-rounded life and stay with his friends, Jeff decides once and for all to put others first and tells his old firm to go screw itself, Shirley and Pierce get their sandwich shop, Pierce takes another couple of baby steps towards being less bigoted, and it turns out Starburns faked his death. Sure, it took two deaths and a near arm amputation to get there, and we still have City College and a loose Chang to worry about, but it's nice to know that for the moment the group got their happy ending.
Troy's reunion with Abed and Britta. In particular, after initially being snubbed by Troy in favour of Abed, Britta's nervously shy expression when she cuts in is adorable.