Just in general, the fact that the students in Black and White will tie themselves into such verbal and mental knots to try to avoid executing innocent people is already a crowning moment of heartwarming when you compare them to 1's students.
There's also a meta-example: Doubt Academy is based off the Dangan Ronpa series, and the Dangan Ronpa series is all about despair, murder, students becoming monsters, etc. The instigator, Monobear, a complete monster if there ever was one, is played by the Game Master of every Doubt Academy Game. And what are these game masters like?...actually, they're very nice! There have been several occasions where someone has been unable to participate in a trial, and the game masters never have any problem with letting this person leave, so they write Hiroshi falling asleep at his podium, or Yukie becoming ill, etc. Or Angelo and Daiki's players have to leave permanently...well, no hard feelings from the game masters, they just write fitting executions to write them out of the story. They are also known to tell off Anons if they do something like one Anon writing a personal attack on the creator of Reisuke because supposedly Reisuke sucks as a character. It seems like a weird example of heartwarming that games about murderers and psychotic teddy bears are being run by administrators who won't accept any real life sociopathic behavior, everyone has to play nice!
Doubt Academy 1
Doubt Academy 2
In Doubt Academy White, the first time an innocent person is sentenced to be executed is in trial 4, when Ritsuka is incorrectly voted as the culprit. Do the students act like Jack back in Doubt Academy 1, coldly telling the innocent Akari to stop defending herself, since it's better this way for everyone's survival? No, this time the students practically fall over themselves apologizing to Ritsuka, reassuring Ritsuka that she in no way deserves what's about to happen to her, and that they very much hope Ritsuka either has a pleasant afterlife or has a more pleasant next life.
During the climax of Black and White, when faced with a Sadistic Choice, both groups of survivors choose to preserve the data of their fallen friends.
The fact that in the "afterlife blogs" opened to the public only after Black and White were already over, a lot of people got to reunite with and/or have a first time hookup with their loved ones. So even in death, some students got to seek happiness in each other's arms.
In Doubt Academy Black, Setsuko's decision to sacrifice herself to be executed instead of sweet, innocent Yukie, who was going to be executed just because Monobear was pissed off at an incorrect suicide vote. Tomiko from Doubt Academy White's decision to sacrifice herself in Larry's placewould count, but unlike the Black example, Tomiko's sacrifice is wasted since Monobear doesn't honor it, preferring to execute Larry anyway.
Doubt Academy 3
In Doubt Academy Alpha, after Dante's player got hit by a car and had to go to the hospital, the mods decided to give Dante a temporary "immunity to death" until Dante's player recovers. Just to make sure the accident didn't screw Dante's player over, the mods decided that Dante was guaranteed not to kill or be killed until the player recovers.
And of course the readers' and other players' immediate reaction to the news...to head over to Dante's blog and drop him well-wishes and prayers for a quick, safe, full recovery.
It should be noted that Dante's player recovered in chapter 2, so in that chapter Dante's "immunity to death" was revoked, and he is now capable of either killing or being killed again.
In Doubt Academy Alpha and Omega, a number of students have Pet the Dog moments related to Usami/Monomi. It's heartwarming that there are more students willing to be nice to the rabbit this time around, since last time the only student who treated Usami/Monomi with kindness (at least on a consistent basis) was Yukie from Black.
Specific examples include Saori, who offers the rabbit a hug after witnessing her beatdown at the hands of Monobear, and Emiko, who outright refuses to call her Monomi (sticking to her original name, Usami).
In Doubt Academy Alpha's first trial, there is evidence pointing to Emiko as the culprit, although it would appear that she is being framed. She's very scared in her internal monologue, as everyone is putting her under fire. Suddenly, Chiemi Shinozaki and Yuu Sagara start yelling and rebuffing the claims that she is the culprit, and before the trial even began reached over to hold one of her hands since the three of them are standing together. Chiemi and Yuu even come up with alternate theories as to who it is in order to make everyone leave Emiko alone. The whole thing is just so sweet and genuine that you really believe that these three teenagers who have known each other for maybe a week would believe in each other the way they do.
Equally heartwarming is the way Sayuri later interjects to say that he can read auras and Emiko's is clean. While this may not be evidence admissible into the court, it's incredibly kind of him to stand up for her that way after just having had himself drawn into the spotlight because of his talent.
He's not the only one who joins in. Shun thinks to himself that if he'd had a moment to speak while everyone was jumping down Emiko's throat he would have pointed out that it's obvious that it isn't her and that someone is framing her. He even shows sympathy towards her when he himself is put under pressure and he wonders to himself if this was how Emiko felt. It's made even more heartwarming when one remembers that Emiko blamed herself for how the fight between he and Chiemi ended, and obviously has a lot of respect for him.
In Doubt Academy Alpha, Nanoka Era, a self-righteous girl with A God Am I tendencies, taking little Kahori under her wing and teaching her about music.
Nanoka gets another heartwarming moment when she reassures Yuuto that among everyone, he's the one who least deserves to die, and his unjust sacrifice will not go unnoticed by the universe, Nanoka will make sure of that.
In Doubt Academy Omega, Imogen comforting Minako and Koyomi after chapter 1's culprit is proven to be Lee, and then Minako comforting the culprit just before the culprit's execution by hugging the culprit very tightly.
Heck, while we's speaking of Omega's first culprit, another moment of heartwarming is the culprit crying tender tears, confessing to the murder, and telling everyone not to blame themselves because she deserves her upcoming execution.
...and Imogen, after Aqua tries to shoo the others away from the culprit to say something to them in private, going Mama Bear and insisting that whatever he wants to say, he can say to all of them.
And then it turns out what Aqua wanted to say was surprisingly something nice; he's actually proud of the culprit for having the "spine" to kill someone before she got offed first, although Aqua isn't proud of the way she went about it, which he thought was dumb. Then, after Aqua tells the culprit he'll remember them as brave, he decides he's being too heartwarming, and suddenly steals a kiss.
Really, the aftermath of Omega's first trial is just one long stream of Crowning Moment of You Are Not Alone from pretty much everyone.
During the first Extended Normaldays of Alpha, Emiko Shiromura's mental state appears to deteriorate completely to the point where, after being confronted by some of the deceased's friends, she attempts to kill herself. The post where this took place was a little ambiguous with the actual outcome of her actions, and almost immediately after it went up there was a round of upset readers who were afraid that she had actually died. The mod of the character in question was quick to reassure them otherwise, but the sheer amount of legitimate concern directed towards said character was an incredible bit of heartwarming in a meta sense.
At the end of Omega's chapter 2 trial, Hikaru and Imogen whisper their "darkest secret" motives to each other. We readers don't actually get to find out what they are, but it's heartwarming that they trust each other enough to do that.
During chapter 4 of Omega, on Rune Andersen's personal blog, Wakana uses her SHSL Onmyouji talent to confirm that Rune is human, and not a monster or spirit that Wakana would otherwise have to exorcise. Wakana's exact words, which in their simplicity have a profound impact on Rune, are "This warmth is human." This is even more meaningful when you consider that the other kids in Rune's childhood referred to Rune as a "monster", which is how they justified bullying him. So Wakana is definitively proving the other kids wrong.
Both Alpha and Omega get a moment of heartwarming in chapter 4, when they both vote "no" on Monobear's "super motive", and thus refuse to sacrifice an innocent member of their group so Monobear would stop his mutual killing game for a week.
Momoko gets one in chapter 5 of Omega when Nicanor escapes a verdict by a very close call, and Momoko is so relieved that Nicanor's still alive that she cries and hugs Nicanor very hard in relief.
In chapter 6, when both classes of survivors meet in Elysium, Minako starts to break down and cry as she realizes that not only will her friends' bodies be moved without her being able to see them or say goodbye, but all the flower crowns she painstakingly made for the departed technically don't exist. Chiemi, sympathizing with her, then offers to take her to where there are flowers so Minako can make the crowns all over again, and even asks Minako to teach her to make some so she can do the same for the Alpha students.
A minor example, but there's something rather sweet about Aqua teaching Minako how to fight, and praising her, in chapter 8, especially considering the bad air between them prior. They even seem to be enjoying themselves! Even later, when there are body discoveries and during trials, Aqua tells Minako to not cry, to be strong, and the narrative describes it as the tone an older brother takes with his little sister.
The best part might be the discovery of Eva's body in chapter 9. Minako steels herself, swearing not to cry this time, and starts investigating. Aqua just turns and leaves, but not before whispering to Minako that's proud of her for doing something but cry this time.
Doubt Academy 4
Very early on in Rotten, the redhead pair made up of P.K. and Rover has two notable moments in fairly quick succession.
The first comes in the prologue, when P.K. finds her guitar (and her whiteboard) and goes to the radio room to play. This is where they first meet, and Rover, who was briefly rather upset about the announcement of a murder game, is ecstatic to see a guitar and praises her talent, going so far as to ask if it's her SHSL. They have a bit of trouble with communication - P.K. cannot speak, and Rover cannot read Japanese very easily. P.K. immediately attempts to write in English instead, and though it isn't quite the best, they can now talk. She offers to let him play her guitar, and without allowing him to point out that he physically, really, can't, hands it to him and acts as his left hand in order to hold down the chords and allow him to play. This moment means so much to Rover that it isn't accurately displayed through words - indeed, Word of God admits not having a sprite that could convey how he felt. The two now appear to be inseparable.
The second comes during the first body reveal. The two of them are witnesses, and were speaking to Yoshiki when he died out of nowhere. Though both of them were absolutely terrified, and their first reaction was to panic, can you guess what their second reaction was? To immediately and fiercely move to protect each other. P.K. stands in front of him multiple times and pulls him away from the body, and when she is coughing and too distressed to do much else, Rover tells off the people who come to interrogate them about what they saw. He even went so far as to glare at Taka, who had only come over to check on P.K.! Their friendship is utterly adorable and defiant in the face of misery.
Also from Rot, there's Malachi's kindness towards Misaki, and hers in turn.
THE WALL. This game is different - the two classes involved are able to communicate with each other via notes stuck on a wall. Most of the notes that were left in the first evening of this option being available are letters of encouragement, uplifting messages, and cute drawings, as well as shared information in order to help the others. Even better since Monobear implied they were competing against each other, and they abruptly brushed it off.
At the end of Rot's seventh chapter, Yoshiki's return, and Jae-Hwa's reaction.
During the trial for the murder of Aya Kamio, Misaki is hellbent on finding the escaped killer of Peko Kimura. This is despite the fact that she had barely known the person in question, and that their last encounter had ended with P.K. punching her in the face. When she succeeds, one can only imagine the way the person she was helping felt. Indeed, it seems that Peko and Misaki have become very close friends over the course of the game, which is coming a long way from their previous belligerence.
There's a short heartwarming moment when the radio becomes relevant. Misaki calls P.K., a girl who had died a week or so beforehand. Though she doesn't believe anyone will answer (because she doesn't believe in ghosts), she still talks about what's going on to thin air as if hoping someone will. Imagine her surprise when P.K. DOES speak back, having regained the use of her voice through death. The most adorable part about this exchange is Peko's utter delight that someone would call her, and her immediate request for Misaki to at least tell Manolo about the radio so she can talk to him again.