Investigations case 5: Detective Badd turning himself in to the police as the last remaining member of the Yatagarasu. Especially painful as Gumshoe, who views Badd as a father figure, is the one who has to make the arrest.
Despite being a... you know, the killer in Case 2 and a member of of the smuggling ring, Cammy Meele, actually gets a minor one when she breaks down and starts explaining what happened, moments before the murder, in a terrified voice, peetering out in the end. As well as the image you got of her killing Hicks. There doesn't look to be any malice or hatred. It honestly looks like a spur-of-the-moment act made out of fear for her life. It can actually bring a little tear to your eye imagining it.
Lauren's reaction to the possibility that she shot Oliver Deacon in the third case of the first game can be modestly gripping (since by this point Lauren has been informed Oliver was really the alias of her ex-convict father, Colin Devorae). It turns out to be untrue, but in that moment when the possibility is still there it still conveys how alone and guilt-ridden she would feel if that were actually the case.
From case 4 of Investigations: Edgeworth presenting a Swiss Roll to Kay, namely the one she dropped earlier. "I was saving it for Daddy." Cue waterworks. Then Edgeworth tells her to let it all out because her father has just died. In the courtroom. Just like his had ten years earlier.
Then again, that moment does quickly descend into a Crowning Moment of Funny. Edgeworth, feeling sympathetic, goes down onto one knee and offers her a handkerchief. She runs forward for what looks like a hug...which is instead her deciding to blow her nose on his cravat. His face is priceless.
Bringing it back into Tear Jerker mode, there's something tragic in Kay freely admitting that Edgeworth and Gumshoe remind her of her dad and Detective Badd.
The whole messed up von Karma family in case 4, specifically the sheer devotion Edgeworth has toward von Karma, blissfully unaware that his mentor was his father's killer. Damn you, Dramatic Irony!
Furthermore, it's clear that Edgeworth and Franziska really do care about each other deep down, but Manfred manipulates both of them. Franziska was really hurt by her father's disregard for her compared to Miles.
Von Karma calling Miles worthless and the long silence that follows is also pretty sad. Becomes a bit of a Heartwarmer, too, when Franziska convinces her father to let them continue their investigation.
Franziska asking her father whether he'd watch her first trial too and his rather dismissive attitude (though the sprites used made it look like he was joking and actually would go to her first trial, not to mention every time she asked if she could do something, he said yes without hesitating). He did seem proud when Edgeworth got his first trial. All of this is kind of sad if you think about it: Sure, he was a villain, but he's a human too, but that more human side is often ignored.
There's a sort of heartwarming tragedy to the whole von Karma family, since Manfred von Karma, for all his many faults, is one better than Bansai Ichiyanagi from AAI2 in the fact that von Karma actually does seem to care about his family. He speaks fondly of his wife and her cooking, seems to dote on his daughter, can remember the name of his granddaughter's dog (which implies he either has a really good memory for things he only hears once or twice, or spends time with his granddaughter often) and remembers her age with no problem.
Detective Badd was probably a lot more upset over Faraday's death than he let on. The game made it sound like he was almost a second father to Kay, so he and Faraday were probably something like Heterosexual Life-Partners. He's really quite a sad character when you think about it.
Crosses over with Crowning Moment Of Awesome, but in AAI Case 5 when Lang, despite finding out about Shih-na's identity and all she's done, still takes a FUCKING BULLET for her.
Badd: You idiot...! What were you thinking, jumping in front of my gun like that...?! What're you risking your life for?!
Lang: I'm sorry, Detective Badd, but no matter what sort of past she might've had... or even if she is a spy, it doesn't change the fact that she's my subordinate. And as long as she is, I can't allow any harm to come to her, not even from you!
Shih-na/Yew: You really are... an idiot... you know that...?
That entire section where you're cross-examining Shih-na because you think she's the murderer was pretty damn harsh simply because of Lang's reaction to it. He's a Father to His Men, and the idea that Shih-na might be a traitor must have been hard on him. He practically begs her to prove them wrong when they're accusing her. And despite that, he still cared enough about her to take a bullet to the thigh for her.
His fully crying animation is... really depressing. Poor kid.
Likewise, Justine's "terrified for her son" animation. The fact that it shows up very suddenly during Logic Chess with her, and she's been pretty much The Stoic the entire rest of the game, makes it hit even harder.
From the same case, there's, surprisingly enough, the real killer's breakdown. The first half of it, at least. The second... not so much.
The Foregone Conclusion nature of the IS-7 Incident of AAI2 from the moment you meet the defendant, if not from the moment Shields begins to talk about the incident. The only truly happy part of the case is that the defendant might finally be released from prison after over 18 years wrongful imprisonment. The downside? The real killer cannot be charged with the murder. It makes you really understand the pressure and power of the Statue of Limitations, and how damned problematic it is. You can actually feel the increasing desperation and mortification the defense team is going through as each and every out they come up with is crushed by the smallest of things, and the Bittersweet Ending is no help.
Of course, all this serves to make Edgeworth's eventual resolution of the incident even more awesome. Statute of limitations? What statute of limitations?
Except, as it was said above to release Master, in the end they're going to be forced to release Gustavia. It really is a catch 22 and one of the driving forces behind the entire game. Either use the knowledge you've gained to release a wrongfully imprisoned man while allowing a murderer to go free, or allow the previous indictment of Master as an accomplice to remain so Gustavia can be put in prison. As the Credits showed Master free, the former was chosen. It's a true Bittersweet Ending. They could finally fulfill Gregory's wish to free Master but at the terrible cost of the loss of justice towards Dane Gustavia. Made Harsher in Hindsight when you realize he's not only responsible for Issac Dover's murder, but due to the neglect of his son, indirectly responsible for EVERY OTHER DEATH IN THE GAME other than Rooke's and has no remorse for any of it.
During Investigations 2, everything about Franziska and her father. When Manfred is brought up by Justine, Franziska's clearly horrified to learn that the thing that got him a black mark on his record was forged evidence (even though moments later it's clarified that he didn't have the autopsy forged, there's still the fact that she's probably realized he really did forge evidence in other cases). The fact that she never knew what caused her father the black mark on his record is pretty heartbreaking itself; this means that neither Miles nor her father ever told her. She knew there was one, but not what caused it. She's also the one who offers the gradually distraught Sebastian advice, however indirectly, by talking about her own experience with a father who did a lot of wrong things in the only time she actually calls her beloved "Papa" "father":
Kay: That person... he really loves his father, doesn't he...?
Franziska: However... one must be able to accept the mistakes of their father... However much they may look up to them...
Kay gains a new Leitmotif when she's met in AAI2 Case 4 that's singularly depressing. She's lost her memory.