This little moment, when Jude first meets Elize and Teepo.
Jude: Are the two of you waiting for friends here or something?
Elize: Friends? We don't have any.
Jude: Well, you do now.
Elize frequently provides these such as in Bermia Gorge, when the party is about to strike the core of the spyrix, she's clearly frightened, but takes Rowen's hand, wanting to stay with the group no matter what.
During a sidequest where Elize tries to remember her parents, she starts decribing a tall man with a beard and feathered hat, then realises she's describing Jiao. It shows how much he meant to her as a Parental Substitute.
At the end of said sidequest the party finds the site of Elize's former house. It's not there anymore, but a bed of flowers is, which Elize's parents planted when she was a child. According to Jude, the flowers mean "precious treasure". It's nice to know Elize's parents loved her, even if she hardly knew them.
Jude and Milla's discussion after they defeat the Master of the Skies. He just wants to be by Milla's side, despite all the danger involved, and she's more than willing to let him.
The night before the group goes to confront the Final Boss, they simply rest up. Elize sees Alvin sitting on a swingset, and goes to sit by him, and he ends up talking about his whole Chronic Backstabbing Disorder quirks: he's more-or-less been raised to be so, so he never saw any problem with it. But now, it may just be too late, and he knows it... but that isn't gonna stop him from trying. He doesn't want to be that person anymore.
In response, Elize just gets up, and kisses him on the cheek. He's startled, but she says she'll be his friend, no matter what.
The conclusion of the "Those Who Act in Shadow" quest is both this and a Tear Jerker.
When Jude's in his Heroic B.S.O.D., Leia is by his side the whole time and even saves him from Alvin attacking them, with hesitation. Jude snaps out of his BSOD and immediately repays the favor by attacking Alvin after she's shot, healing up/caring for Leia afterward, and then thanks her for helping him the whole time. note Becomes a bit of Fridge Brilliance for Jude/Leia shippers once they realize that Leia's bandages are under her clothes, meaning Jude had to undress her to patch her up. As a medical student, this may not his first experience seeing such things, but the fact remains.
Alvin and his cousin Balan reminiscing about his mother. Specifically a story about how, when Alvin was a child, he wanted to give her a flower crown made out of a rare clover. Since he couldn't find them, he just painted normal clovers the color of the rare ones and gave it to her. Unfortunately he didn't let it dry and the paint got into her hair, after which he started crying and hugged her at which point it got into his hair. It's a heartwarming and cute story that shows that Alivn wasn't always the suave, backstabbing mercenary type.
The resolution of a sidequest about Rowen's ex-fiancee who he believed died in the Battle of Fezebel Marsh 20 years ago. It turns out she arrived on Elympios and suffered from amnesia, ending up Happily Married and has a daughter. Rowen is just happy knowing that she's alive and reunites her with her husband who was stranded on Rieze Maxia and wishes them well. In the end she remembered him, so he could move on and be happy for him.
Despite repeated incidents where he ends up on the opposite side of the main party, Gaius remains respectful and treats all of them with kindness. The main party returns that with their own respect for Gaius showing. As far as either side is concerned, the only conflict in the end is their respective plans to save the world differing.
Gaius: If you continue Jude, you'll lose the person most precious to you.
Jude: (looks at Milla) If I backed down now, I'd never be able to look her in the eye.
Muzet: Milla. You already have something to protect.
Milla: (looks at Jude) I wouldn't be able look him in the face either if I stopped.
The ending, and the "Where Are They Now?" Epilogue that follows it. Gaius and Muset are redeemed, Alvin finds honest work, Leia is helping support her family, Elize is going to school and had made friends, Rowen is the new Prime Minister of Rize Maxia, Jude works on Spyrite research to help Elympios and Milla is proud of her new role as Maxwell. (And it's implied that she and Jude are able to keep contact)