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."
From the Pilot, "I see your value now"
Jeff changing "Hot Blonde Spanish Class" to "Britta" on his contacts list.
The entire resolution in "Environmental Science." Troy faces his fear of rats to help Abed out after leaving him out to dry, Pierce helps Shirley to overcome her difficulty in public speaking, and Jeff reunites the Changs to make up for screwing the study group over (It Makes Sense in Context).
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".
Abed and Troy building a memorial towards Pierce's deceased mother in "Conspiracy Theories and Interior Design".
The scene following Jeff's statement that everyone in the group is a sexual prospect for one another in Romantic Expressionism is mostly hilarious, but the look on Jeff's face when he looks at Annie is so different from how we've seen him so far in this series, that it pushes over into heartwarming, even if you don't ship them.
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.
Pierce of all people coming back to accompany Abed before the rest of the group does.
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.
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 simply 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.
Even after Pierce forces his way into the game and kicks Neil out of his seat, Neil still has his character give Pierce's character his cloak for warmth (since Pierce was hurriedly given a character that had no weapons or clothes after he barges in).
At the end of the episode, Neil and Pierce part on good terms and agree to have another game sometime, since Pierce' forceful intrusion into the game made it the most interesting one Neil's ever had.
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.
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".
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.
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.
In general, with a few exceptions the cast and crew of the show really seem to get along very well with each other, enjoy making the show enormously and particularly seem to enjoy engaging with their fans.
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: We've only been playing this game for a few hours, but you've been playing it your whole life.
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 development, even if he does allow his inadvertent racism to cut in.
Britta: We apologise for him. Gilbert: No, it's okay. He's family.
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.
At the end, when Abed comes back to download Hilda onto a USB drive.
Apparently Dan Harmon planned to have a heartwarming moment between Pierce and Abed where Abed made a mod of the game for Pierce where he played catch with his approving father which would have resulted in Pierce hugging Abed. Unfortunately, Chevy Chase walked off the set early and the scene could not be filmed, later leading to the feud between Chevy Chase and Dan Harmon.
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.
In Virtual Systems Analysis
Abed!Dr. Shirley: Abed's been filtered out because nobody needs him.
Annie:I need him!
Shirley's sons disguising themselves as Abed's cousin so she could get a turn in the bouncy castle on family day.
At the Inspector Space Time Convention, Abed's penpal goes crazy when Abed chooses Troy over him, and the penpal locks Abed in a phone booth. Abed starts his normal freakout and shouts "Troy will come for me!" Then realization dawns on his face, and he calms down.
Abed: Yeah. Troy will come for me.
And, of course, Troy does.
Abed: In my long history of being locked in things, that was the first time I knew somebody would come for me.
Jeff assuring Annie that, if they were married, she'd never find him flirting with some random woman at a bar, after she's spent her time at the hotel pretending to be married to Jeff whilst he was flirting with a woman at the hotel bar.
The ending of "Cooperative Escapism In Familial Relations." Jeff makes a big Thanksgiving spread for everyone, and even brings the Dean in to join the group for the meal.
Jeff thanking Britta for making him confront his father before sharing a heartfelt hug with his half-brother.
The end of "Herstory of Dance", after Jeff has spent the entire episode smugly waiting for Britta to fall on her face after planning a "Sophie B. Hawkins" dance that everyone expects Hawkins to appear to, Pierce reveals that he called in a favour with Hawkins to get her to show up and save her dance:
Jeff:You did this? But why? Pierce: Because, Jeff, in the face of all logic and reason, Britta didn't back down. Jeff: That makes no sense. Pierce: Also, I didn't like the way you were being such a jerk to her. Jeff: She was acting crazy! Pierce: Yeah, but what choice does she have? You make fun of her. You use her name as a synonym for screwing up. Cut her some slack, Jeff. She helped you reconcile with your dad. For Pete's sake, let her be happy.
Jeff's subsequent text to Britta:
Jeff: I know it’s probably impossible to read my texts without them sounding sarcastic but, I assure you, this one is as earnest as they come. Congratulations on an awesome dance, you Britta’d the hell out of this thing.
This one from Twitter, but Jeff sends a Tweetnote Which is itself a Call Back to Season 1 episode "English as a Second Language" where Jeff mentions that very reservation. to the entire study group:
Jeff: A long time ago, I made a reservation for tonight. Steak dinner. Alone. But now I've changed my mind. Would you join me?
And then Annie's response.
Annie: We were going to join you anyway, duh doi.
Pierce's hologram talking about how, for all of it's flaws, the main reason Greendale is crappy is because it allows crappy people to come & try to sort themselves out, and for that reason you shouldn't turn your back on the school.
In a meta-sense, it's also an indication that for all the media hoopla over the feud between Chevy Chase and Dan Harmon/the rest of the cast and crew, ultimately relations between them aren't irreparably bad.
Pierce's final messages to Troy, Britta, Annie & Shirley show that he truly did respect & care about them.
Mr Stone: (to Britta) Did you know that you hate yourself more than you should, and that your passion inspired me?
Mr Stone: (to Shirley) Did you know that you are not only a credit to your race and gender, but to our species and that I was intimidated by your strength of character and business acumen? note Shirley: Yes.
Mr. Stone: (to Annie) Did you know that you were always my favorite?
Mr. Stone: (to Troy) Did you know that you possess the greatest gift that life can give: the heart of a hero?
The ending of the "Floor is Lava" episode as Troy says goodbye to the group.
Abed: By the way, when I cloned you, I had to patch some missing parts of your DNA with genes from a homing pigeon. You may notice side effects, like the compulsion to come back.
The resolution to Duncan's attempts to seduce Britta in "Bondage and Beta Male Sexuality". Namely, that he doesn't take advantage of her, actually gives her decent psychological advice while she's having an existential crisis, and manages to validate her existence.