MOMO meeting her father, Joachim Mizrahi, and learning that he wasn't the Mad Scientist that people thought he was.
Butt Monkey of the series Allen gets one of these (and a simultaneous Crowning Moment Of Awesome) in the third game of the series. Having had absolutely enough of being the powerless joke that EVERYONE considered him to be (whether they said it or not), he steps forward to stop a fight between the party and a duo of Shion and Kevin, who was Not Quite Dead and had used Shion's love for him to bait her into betraying the others. Calling Kevin out on his BS, he gets cracked with a blast of energy, and sent flying backwards. He gets back up, walks toward Kevin, finally confesses his feelings for Shion, and gives a speech that seems so cheesy, but coming from this specific character, it works perfectly. KOS-MOS joins the scene after Kevin cracks Allen again, and finally, Shion figures out who really loves her, and rejoins the team for the game's That One Boss battle. As cheesy as it was, this troper couldn't stop crying.
After Shion's passed out from U-DO exposure, Jin comes into see her after she wakes. After a short conversation, Jin finally says that 'as long as you're all right' he won't object to her working so hard, and leaves. Then, you and Shion notice that he's left behind a packet of herbal medicine (as he was a doctor for a while), and Shion smiles as she remarks that he didn't have to do things in such a roundabout way. D'awwwwww...
During the end of Episode III:
Shion (hugs KOS-MOS/Awakened Mary): "I'm so glad...to have had the chance to meet the real you."
No love for the Mizrahi family? Two very heartwarming scenes: this and this
Kind of more of a Heartwarming In Hindsight but in another game, Project X Zone, KOS-MOS (as Mary Magdalene with the blue eyes) tells the party who lives on Earth, "Farewell, dwellers of Lost Jerusalem." She finally found the place.
During Episode 2, after Albedo's been attacked by Patriarch Sergius, Rubedo/Jr.; his brother, rushes over to him as if to make sure he's okay. It just goes to show that even IF they may hate each other, they're still family...
Some tropers may disagree with me, but the fact that even after mind raping her TWICE, using the Terms of Endangerment "Ma belle peche" around her and possibly even doing... things to her, MOMO STILL forgives Albedo and tells Rubedo/Jr. to say hello to him for her! D'awwwwwwww!
From the first game, there is something touching about Margulis' reaction to Cherenkov's death. When he is told that Cherenkov's marker disappeared in an area occupied by Gnosis, Margulis' just stares at the soldier giving him the information, and Pellegri has to instruct the soldier to finish the rest of the report. Margulis, who had spent the entire game thus far coolly dismissing the deaths of others including those of over a billion people on planet Ariadne, effectively BSOD's over Cherenkov's. It's somewhat endearing.