Onikakushi-hen, the gang's "punishment" for Tomitake.
Shion who is actually Mion dressed as her sister brings Keiichi lunch when he's on the brink of passing out. She tries to apologize for her sister, but Keiichi tells her to tell Mion to not worry about it, as it was part of the club, and she leaves with a smile. The visual novel is more detailed in this scene, as Keiichi is almost brought to tears every time he takes a bite. It's almost romantic, but it shows how much Mion cares for him. This is possibly also after Mion told Shion about the doll, showing she wants to forget about what happened and, is slowly showing her girly side in the process.
In the Watanagashi-hen manga, Keiichi starts crying after Rika and Satoko go missing because he thinks that it's because he told Rika about going into the Saiguden with Takano, Tomitake and Shion. He refuses to tell Rena and tells her that she will disappear if he tells her. Cue Rena hugging him and saying "Rena won't disappear."
In Meakashi-hen, although it is an early sign that Shion has Hinamizawa Syndrome, when Shion first hears the extra step and belives that it's Satoshi, after a mental conversation with him saying that he'll stay with her and lend her his strength. I couldn't help but think how heartwarming that was, even after thinking "Oh shit, Shion's going insane"
During the Atonement Arc, the support Rena's friends give her after they find out that Rena killed the people who were conning her father out of a substantial amount of money. They tell Rena that she could have and should have come to them for help, and they make themselves come to terms with how Rena responded to her situation. Lastly, Rena's friends help her hide the bodies. Of course, they should have reported Rena to the police and made sure she got psychological counseling, but they got most everything else right.
Speaking of Tsumihoroboshi-hen, there's two of these within the same episode: when Keiichi confesses to his True Companions about the toy gun incident (to which Mion tells him that there's nothing wrong with hiding embarrassing parts of your past and Satoko reassures him that he's a great guy with nothing to be ashamed of), and when he apologizes to Mion for killing her in Onikakushi-hen, despite her not remembering:
Keiichi: "I will never distrust you, no... I will never doubt a friend, ever again."
The last episode of the first season has Rena prepared to kill everyone in the school because she's suffering a delusion about an alien invasion. Keiichi disables the makeshift time bomb she set up and challenges her to a fight (his baseball bat against her billhook), and although she's clearly willing to kill him, he peppers the duel with friendly banter reminiscent of their water gun fight earlier in the series. When she disarms Keiichi and pins him down, he tells Rena to finish him off, and instead she breaks down and cries at the realization of what she's done. He hugs her and tells her everything's going to be okay. It was enough to bring Creepy Child Rika to tears.. Their whole dialogue just before the end of their fight and the way he manages to snap her out of her paranoia by tauting her as if it was a game is impressively well-rendered, especially in the sound novel.
Keichi: What? You want me to be your maid? That's something… Rena: You don't need to be my maid but… the rest is the same… I want you to say "good morning" to me when I wake up and "good night" when I go to sleep. I want you to treat me gently and make me laugh. Hm? Ahahahaha! I guess no matter who wins, we'll always be… together. Keiichi: Yeah… we'll alway be together. […] Rena… even if we die, we'll meet again in another life. When that happens… Rena: Yeah… we'll laugh in a normal way. We'll have fun in a normal way… and we'll fall in love in a normal way. We'll never doubt each other. We'll always trust each other.
Lets face it, Minagoroshi-hen has a lot of heartwarming moments. The first one one though (especially for shippers) is when Keiichi wins the doll after altering the "destiny" of the toy shop contest. Keiichi then starts handing the doll over while Rika tries to stop him, but instead of giving it to Rena (and thus causing Shion to eventually go crazy), he gives it to Mion, who tries to point out that she's not girly enough for dolls, but Keiichi says that even if she's a Tomboy she's still a girl to him. Cue Mion becoming more feminine and Rena wanting Mion to accept Keiichi's wish.
In Minagaroshi Rika has finally found out who killed her. In a CMOA she refuses to be drugged so she'll remember who it is that kills her this time, and as she's being butchered alive the spirits of her friends who died protecting her in this arc surround her and promise to help next time.
Minagoroshi-hen, where Keiichi decides that if they can't get Child Welfare's help to save Satoko from Teppei with just the five of them then the help of the ENTIRE SCHOOL caring about and advocating for her must be the trick. Bonus for Rena when there's too many of them to fit the typical conference room: "Please arrange a larger room... It's the room that should be adjusted for US."
When even that doesn't work, Keiichi gets even more support by rallying the staff and perverted customers of Shion's restaurant. When this catches the attention of Oryo Sonozaki, whose family owns the village and hates Satoko's family, Keiichi personally threatens her before humbling himself, to beg for her help. Oryo is impressed enough to actually lend her support, and just about the entire population of Hinamizawa turns out to help as well, even setting up signs on the side of the road to beg motorists to help. Finally, the snobbish head of Child Welfare listens to them and calls Satoko one last time. Keiichi tells Satoko over the phone about everything they've done to help her, causing her to finally give in and ask for help.
When Keiichi is shot by Takano. From his being shot to his death, not matter how heartbreaking this moment may be, you see just how much his friends really care for him.
The scene right before that when Rika is prepared to die protecting Satoko and realizes how important her friends are. Then Keiichi, Rena and the twins come out of NOWHERE and save them both. Then they all kick butt.
There was also, in Minagoroshi-hen, where the ghosts of Rika's recently-slaughtered True Companions try to comfort her as she is being disemboweled by Takano.
In Minagoroshi-hen, the fact that when Rika suggests siccing the Yamainu on Satoko's uncle to keep her safe Irie is willing to go through with it, despite Takano pointing out that this could endanger his career. At first it just sounds like the drastic action so often taken in Higurashi, but then you realize that beneath the perviness and the claims of needing to keep Satoko alive to further his research on Hinamizawa Syndrome, Irie really, really cares about her.
The end of the last arc, as it is the only arc where nobody dies. It's very rewarding after having sat through many arcs in which people die in pretty horrifying ways.
Rika really puts it in perspective;
Rika:Takano and Hanyuu, were you listening to what Mion said? We don't play Old Maid. Just Old Geezer. Takano laughed it off as being the same but it is a completely different game. After all, if one adds the missing card that is taken out in a game of Old Geezer, it becomes a game without losers.
Rika: After adding Hanyuu, our missing card, the world became a world free of losers. It is the height of folly to purposely take one card out of the game. This world doesn't need a loser.
There's a part towards the end of Matsuribayashi-hen where the group thinks that Shion has been killed (she hasn't), and Satoko calls her her "Nee-Nee", admitting that she thought of her as a surrogate sister, which causes Mion to embrace her and break down. The effect is enhanced by the knowledge that in Watanagashi-hen and Meakashi-hen, Shion killed Satoko in a particularly bloody and sadistic way.
In Matsuribayashi-hen, the reconciliation between Ooishi and Akane (who regularly brings flowers to the dam site manager's grave, despite having fought him fircely during the conflict) is a surprisingly sweet moment. It's made all the more heartwearming that Ooishi just understood he has been fighting the wrong enemy for four years.
At the very end, when Rika finally turns the calendar to July 1. The relentless tension of the entire series to this point makes that simple act very satisfying.
At the very very end Miyoko completing her flag collection and her parents surviving the bus crash. Due to Bernkastel's intervention also saving her from the orphanage.
Like one of the comments on Dear You — Bond video says: "The world decided that they had to die. They told the world to go fuck itself."
The properly named "Kokoroiyashi-hen", aka Heart Healing Chapter. It's even post Kai.
Rena confessing her feelings for Keiichi in the last OVA. Rival shippers may not find it cute, but the scene certainly is both cute and funny (Rika shows her dislike of romance), with all the blushing.
The alternate ending, Miotsukushi-hen also has this really sweet scene where Keiichi, in answering an interrogation by Rika, recounts how he gained forgiveness from one of the girls he shot at with his model gun and then goes further and lets Rika know that he remembers when she forgave him for what he did in Onikakushi-hen. The scene that ensues brought Rika to tears.
How about the change in the opening credits of Kai? All season we've seen Rika stop, turn around, and wave at the camera towards the end. After Minagoroshi-hen, we see that she was waving at Hanyuu, who promptly runs over to catch up with the gang.
The last Kira OVA features a much younger Rika who somehow ended up in the present. The scenes between her and Hanyuu are absolutely heartwarming. Especially the part where Hanyuu tried to keep the younger Rika from going home to all the cycles of despair that would await her. Younger Rika's response? She was willing to go home because she wanted to see Hanyuu again. Cue "awwwws."
The manga-only Hinageshi-hen chapter is a cross between this and a Tear Jerker. Mion has gone to a cram school away from Hinamizawa to get into Tokyo University, but stress and homesickness makes her do badly. Returning home out of desperation, she ends up believing that the rest of the club is plotting to kill her. However, it's cleared up as a misunderstanding, and no-one dies. Mion starts crying in happiness that her friends are still with her... Cut to the real world, where it is revealed that Mion has been catatonic after the Great Hinamizawa Disaster. Oiishi and Akasaka are at her side, having tried to question her. As her body starts crying, Oiishi says that it is the first time she's reacted since the disaster, and that they should leave. He notes that a flower placed in a nearby vase (a hinageshi) has faded. As he tells Akasaka, the meaning of a hinageshi in flower language is 'consolation'.
Narration: That girl surely won't return to this world anymore. But that girl is certainly saved... in the dream...