"Welcome back, big bro! I wanted to see you so much!" Admit it, seeing Nanako again made you all warm and fuzzy inside. And afterwards, Yu having dinner with Nanako and Dojima and his inner monologue mentioning how much he loves them, that's just icing on the d'awe-cake.
During Aigis' ending, her conversation with Labrys in the limo after she finally realizes that the indirect reason she met P3's main character at that pier was because she had unconciously inherited Labrys's sincere wish that her successors could meet someone they loved and truly be happy. When Aigis thanks Labrys for this, telling her that her wish had come true, and Labrys begins to cry, I admit I teared up right along with her.
In the stories of Yosuke, Chie and Yukiko, they get confronted by their Shadows (actually the Malevolent Entity), who proceed to rip their resolve a new one, telling them that they want the P-1 Grand Prix to happen because they want to feel needed or avoid boredom again. They're on the verge of falling to despair and reject their Persona again, until Rise gets the rest of the team or whoever's available to support the character that this time, they got friends to support them even during bad times in question, bringing resolve back to them and kick their Shadows' asses again.
The sequence where Labrys accepts her Shadow and befriends the main cast, in pretty much any of the story routes.
Teddie's route, after the fight with Naoto. He was really torn up by her illusory words, so making up after the fight was satisfyingly sweet.
In Elizabeth's route, you learn that Minato's Heroic Sacrifice in the third persona game was not a complete sacrifice. He's not dead, but in a deep slumber, and Elizabeth now works towards awakening him.
Also at the end of her route, after Curbstomping Yu in a fight, the rest of the investigation team shows up and threatens to fight Elizabeth for hurting him. Shows how much of True Companions they really are.
At the start of Yosuke's story, he decides not to call Yu up & tell him about the return of the Midnight Channel because he didn't want to panic his best friend by telling him the Midnight Channel was back whilst he was out of town & unable to help.
When Yu is forced to fight a wicked-speaking Yukiko, she summons her Persona, which Yu observes. He knows she is not herself, thiking "the real Yukiko should have a beautiful heart like this."
In Akihiko's ending, he tells Mitsuru that he's going to leave the Shadow Operatives eventually, as he can't stand by & let small crimes go unpunished whilst he's working towards a larger goal, as he is now. Mitsuru's reaction effectively boils down to "That's it?", showing that she knows Akihiko well enough that she'd already figured that out. She goes onto say that they'd be able to work something out so that Akihiko work for both the police & the Kirijo Group, and he shouldn't underestimate his value to the group.
In Yukiko's story, she and Labrys stop by a classroom to get some character development. Labrys start talking about her looks, and Yukiko decides to help her. When she's done with the make up and whatever Yukiko brought with her to the TV World, Labrys can only mutter "I never thought I could be this pretty...". Given the Broken Bird aspect of Labrys's character, this little moment is one of the sweetest Yukiko has with other character in the whole game. Made even better when Yukiko goes to Junes to buy fashion stuff for when Labrys comes back.
Remember the Bittersweet Ending of Persona 4, where Yu has to leave his friends? Yeah, like THAT was gonna last. That final line from Yu's story mode is sure to brighten the day of any player of Persona 4: their story isn't over just yet.
Yu: The Investigation Team is back in action!
Yu referring to Yosuke as "Partner." Whilst this is Yosuke's nickname for Yu in the original game, it's good to see that Yu does the same to Yosuke - he actually does consider Yosuke his partner, very fitting for the two who started the Investigation Team in the first place.
It was a really small thing, but at the end of Teddie's route when Labrys is leaving, Teddie starts to get upset, and Yosuke, without prompting, starts to scratch his head in a form of comfort. It's small, but when you think about it it's actually really sweet.
"Damn, out of time? At least Koromaru got some good exercise."
There's also Chie's adorable admiration of Akihiko.
Examples from Ultimax:
Ken truly does care about Koromaru, and one of his finishing poses has him petting him.