For all of Chapter 3, Agnes has been pushing her friends away and generally acting like a jerk to them, to the point where even Tiz has to call her out on it. Then, on their way to the fire temple, the cavern breaks apart and Tiz and Egil are hanging over lava and Edea and Ringabel can't pull them up. Everyone, including Airy, is telling Agnes to go on ahead. Does she? No. She pulls a Crowning Moment Of Awesome, rescues Tiz and the apologizes to everyone for her behavior. It is at this point that the heroes become True Companions
After you defeat Barbarossa the Pirate, you can see his ghost haunting the Ghost Ship with the other dead crew... and he seems to be enjoying himself as always. Given that he was an extremely likableAnti-Villain, it's nice to see he's happy even in death.
In a late-game Party Chat, Agnes is revealed to no longer be a vegetarian. How did this happen? Apparently, sometime between Chapters 2 and 3, on the way to Eisenburg, the party ran out of supplies and was forced to spend their days fishing for food. One night, Tiz prepared a meal for Agnes only to have her refuse it. Ringabel has a little one-on-one with her both about Tiz preparing the meal for her, and about the fish sacrificing itself so she could live and she takes those words to heart. What makes this particularly heartwarming is that it this occurs while Anges is grieving over Olivia and hostile towards the party, and Ringabel is subconsciously remembering Braev telling him this long ago.
When you first walk into the central healing tower, there is a little girl and a nurse next to her. Talking to the nurse reveals an anonymous man had, for the last year or so, been sending money to keep the little girl alive, and the nurse is very happy because the girl is now healthy and, with the money that had been given, was allowed to live in the hospital. If you look closely, her hairline brings to mind someone you've met... This is Ciggma Khint's daughter, whom you have unknowingly saved by killing off Jackal and Profiteur, allowing Khint to make money from the Kingdom of Anchiem by the King himself.
Holly and Barras slowly become closer over the course of the game. After one fight, you leave, but they just get up, as Holly quietly cast Reraise on them both during the battle. They're too weak to fight, but not too weak to spend the night together under the stars. Even better, Ringabel and the others noticed her casting Reraise, but they didn't finish them off because they were too adorable.
Whenever the Jobmasters team up
Barras and Heinkel backing up Ominas.
Jackal coming to Praline's aid.
Of course this means bad news for you.
In the later world loops, Braev increasingly becomes more forgiving to Edea, up to the point where he tells her that he's proud of her having grown up and finding a cause to fight for, which contrasts his attitude in earlier iterations where he refuses to see reason. Also, any interaction between Braev and Alternis. When Braev reveals that he's always considered Alternis his surrogate son, Alternis is shocked and deeply touched.