Most of Abed's Uncontrollable Christmas counts - Professor Duncan crosses the Moral Event Horizon over Abed dredging up memories of his deadbeat father; Britta is shunned by Abed for genuinely wanting to help him and being misunderstood.
In "Aerodynamics of Gender" when Abed is bitched out by Meghan. What makes this moment so tear-jerking is not that she said it, but the fact that Abed wrote it, meaning that Abed really believes that he can't relate to anyone in some way.
The Dean's breakdown in "Documentary Filmaking Redux". Turns out he didn't even go to Greendale, he went to an actual university and he felt like he was ashamed of Greendale, and wanted to make it better.
Pierce's home life in a fridge way. Before his mother died in the third ep of season 2 it was just him and her with maybe a few visits from his Jerk Ass father who passed down his prejudices. His seven marriages could be just his desperation to not be alone but for many reasons the marriages couldn't work, his "Super Fertility" is just a euphemism for being infertile (Which may relate to why he sees Jeff and Annie as his faux son and daughter), his friend Troy got to live in his mansion in season 2 for free before moving out (Since Troy's an idiot he had no idea that he was addicted to pills until it was too late) and didn't express much gratitude and from the season 2 finale that summer and most school breaks are just days to wait until the new semester.
Chang's Imagine Spot of him hanging out with the study group in "Accounting for Lawyers". He's in a Pop 'N Lock contest by himself because they were late and it feels like they abandoned him.
Especially since after all his hard work, the group rejects him anyway when they finally do show up. The single, pained tear running down his cheek.
Britta's breakdown in "The Science of Illusion" where she tearfully reveals that she was behind the backfiring April Fool's prank that caused all the trouble in the episode because she just wanted to be wacky and fun like her friends for a change. Since they'd all been ragging on her for being a buzzkill (Jeff especially), they all look rather guilty. It then sets off a chain reaction of weepy confessions of feelings of inadequacy from everyone except Jeff and Abed, which are all quite sad — until, of course, we get to Troy's.
Troy and Abed completely turning on each other in Pillows and Blankets. Abed sends an email to his troops detailing Troy's weaknesses - including his insecurity about his intelligence, and the fact that it's incredibly easy to make him cry. Troy tells Abed that he'll never get another friend, because nobody will have the patience with him that Troy had.
At the end of the episode, the two of them both want to keep fighting, because they're convinced it will be the last thing they ever do together. They would rather beat each other with pillows indefinitely than go their separate ways, but they don't see how they can just go back to being friends.Until Jeff intervenes.
Kind of a fridge tear jerker: Abed seems pretty upset (for Abed) in Regional Holiday Music, and he's desperate enough to spend Christmas with his friends that he resorts to recruiting them for the glee club pageant. It seems funny at first - and then you really look at him in certain scenes, like right before he and Mr. Rad start singing, and when he's apologizing to the rest of the group and saying he'll see them all after break, and he looks/sounds like he's as near to actually crying as he's ever gotten. And then you remember that last year, following a complete mental breakdown, Abed decided that the new meaning of Christmas for him is spending time with his friends.
Abed: We're inside a locker. It's where I spent a lot of time in junior high.
Annie: You think this is where we'd put you? You know that's absurd, right?
Abed: Well, I'm not stupid. You can see I've upped the square footage. It's a metaphorical locker. It's a place where people like me get put when everyone's finally fed up with us.
Gilbert Lawson discovering that his father never cared about him, and will only let him have the company if he agrees to never tell anyone who his parents are.
To elaborate, Lawson is black and his father is Pierce's more racist father Cornelius. So imagine spending your whole life mastering your father's game and winning and being presented with a legal document that makes it illegal for him to say who his real parents are. All because it would tarnish the pure Hawthorne name.
It's made worse, after Gilbert refuses to sign the document saying he'll never tell anyone who his parents are, and virtual!Cornelius attacks him in response, by Gilbert's pained scream of "NOOOOO! I'M YOUR SON!"
The study group deciding to help Gilbert.
Jeff: We've been playing this game for a few hours. But you? You've been playing it your whole life.
Followed by Pierce's "You took all his crap and you never even got to take his name. But now it's time for your reward, brother."
Sure, it was played for laughs most of the time, but Troy leaving the study group due to sacrificing himself to the Air Conditioning Repair School still feels pretty sad, particularly where Abed can't even face the study group anymore when he mentions that Troy told him as a parting word, "I know you hate this when people do it in movies."
Near the end of the Season 3 finale, when we see Abed destroying the Dreamatorium.
But also sort of a fridge heartwarming, as it demonstrates that he realizes that perhaps he has some maturing to do. And he did keep a few panels of it, and built a smaller one.
After watching "Curriculum Unavailable", everyone's anger towards the dean in "Course Listing Unavailable" becomes this. He sent his assistant home because she wore the same clothes as Annie, he made a little song for the gang during the announcements, he saved them pizza on pizza day, he just all around loves the group (to the point of great annoyance).
In "History 101", Abed realises their time at Greendale is ending and takes it that the group is splitting up, so he retreats into his mind where their life is a Sitcom with a Laugh Track and Status Quo Is God. The more things change in the cafeteria, and the closer Jeff comes to victory, the further in he goes.
Jeff revealing to his father in "Cooperative Escapism In Familial Relations" how supremely screwed up he is.
"I am not well adjusted. And more often than not, I am barely keeping it together. I'm constantly texting and there's no one at the other end. I'm just a grown man who can't even look his own friends in the eye for too long because I'm afraid that they'll see that I am broken. So you get credit for that. One time when I was in seventh grade, I told everybody in school that I had appendicitis. I wanted someone to worry about me. But when Beth Brennen asked to see the scar, I didn't want to get found out so I took mom's scissors and I made one. It hurt like hell. But it was worth is because I got 17 cards and I still keep them in a box under my bed 22 years later, because it proves that someone at some point cared about me. You wanna see the scar? So. You get credit for that too. This is me."