The part in Apollo Justice where Mafia heir Wocky discovers that the decision of his father to go straight, a decision Wocky had loathed, was done because of his father's desire to protect him.
Made even more heartwarming by the fact that Wocky just can't quite accept it. He stutters, then returns to his normal "gangsta" sprite and disappears. Switches to a CMOF when his father reveals the new family enterprise to be a bakery.
The moment at the end of the 4th case of Apollo Justice where, playing as Juror #6, you choose whether the defendant is guilty or innocent. As the juror leans over the touch screen, their face is reflected in it- Lamiroir, the amnesiac singing diva from the third case. Then, after you press the button her sleeve slips back, revealing a familiar bracelet on her wrist. As the realization sinks in it's simply amazing- her true identity, which she'd forgotten for years, is Thalassa Gramarye, the mother of both Apollo and Trucy, long believed dead. Then you realize Phoenix had planned this all along and you're simply lost in awe.
During the end credis sequence of Apollo Justice, there is the scene with formershut-in Vera Misham.
Vera: I've decided to keep painting. Originals only, of course. I suppose I'll have to see a bit of the world outside to find out what to paint. But, I know there are good people out there, now. I've met them. She draws in her sketchpad and reveals a sketch*
... of you, and Trucy, and Phoenix
. Vera: The door is open. The world is waiting. Thank you.
Even more heartwarming when you consider what you learned during the investigation: the rough sketches underneath the paintings were of Apollo's cases, and her father, who played a role in Phoenix's disbarment, admired Phoenix greatly. Despite her limited understanding of what she was asked to do and why, the Mishams were always on your side.
The end credits of Apollo Justice, when you see Phoenix. Goes something like this: "You know, I've been a piano player longer than I've been a lawyer now. Maybe I'll start taking lessons. Or maybe I'll take the bar exam again." The screen pans out to reveal a photograph of Phoenix floating down, with Phoenix giving the most sincere grin the player ever sees. Absolutely nothing in this game made this troper cry until that moment. He's just so...happy.
Am the only one who finds it touching that in Apollo Justice, the Judge gets a couple of lines that seemingly indicate that he himself never believed that Phoenix had been forging evidence, and that he had faith in Phoenix? He's the last character from whom you would expect Character Development, but it's clear that he has developed, in a sense: he's come to hold Phoenix in high regard.
Judge: You do belong in the courtroom, after all.
The Judge wouldn't have had anything to do with Phoenix's disbarment (the Bar Association voted to decide the penalty), so it's probably the first time The Judge gets to tell Phoenix that Phoenix is a true attorney.
Half this, half CMOF with all of Apollo's baffled responses to them.
And then we have a freshly disbarred Phoenix and an eight-year-old Trucy in the MASON system. Phoenix is so awkward and unsure of how to be a parent, but he still comes to the firm resolution to look out for this little girl. One of the most notable exchanges in this scene occurs after Trucy tells Phoenix about her mother's mysterious disappearance in a magic trick several years ago. Considering that her biological father also just vanished two weeks earlier...
Trucy: Hey, Daddy? You won't...
Phoenix: Don't worry. I won't vanish, I promise.
It's not an explicit callback, but it does seem to reference Phoenix's first meeting with Maya, who was also suddenly left alone in the world — and Phoenix hasn't changed. He told Maya he would defend her because he couldn't abandon her and he believed in her innocence, and he makes the same promise to Trucy.
Apollo's reaction to Trucy's abduction from the courtroom, in Case 4-2. He's so happy to see her safe that he starts crying. He then angrily threatens to drag the guy responsible to court. It then becomes much more funny when Trucy reveals that the guy was her ventriloquist dummy, leading to Apollo threatening to drag her to court.