Grace adopting an abused puppy that was being groomed for dog-fighting, at the end of one side-quest in Case 6.
At the end of One-tooth Sam's side-quest in Case 11, he vows to make Cooperville a better place to live in honor of his late wife's memoryafter getting back his lost wealth.
When Jones is out of commission halfway through Case 31, Ramirez steps in to be your partner. He's genuinely worried about Jones despite how hard the latter is on him. It just goes to show how much of a nice guy Ramirez is throughout everyone criticizing him constantly which is likely what helped make him so popular with the fans.
Ramirez: Oh, <Rank> <Name>, you've seen Inspector Jones? How did he look? Do you think he's going to make it?? I'm so worried about him... You know, Jones was the one who helped when I started my work as a policeman. He was like a mentor to me! Oh, I know he likes teasing me, but he's got a good heart. And, well, I still have many things to learn, after all!
At the end of one side-quest in Case 41, Cathy King (Chief King's granddaughter) confesses that all she wanted was to dance with a nice guy at her prom ball, which got ruined by the actions of the Rorschach Reaper. She then asks Alex if he'll dance with her. Jones helps.
Alex:(blushing) A-a dance? With me? But—but there's no music! And no ligh—
Jones: Of course this idiot would love to dance with you, Cathy! Go on, have fun! (to the player) Come on, (player's name). They need some space, and I've seen the piles of burgers on the buffet table! It'd be a pity to let them go to waste!
At the end of Case 28 of Pacific Bay, Amy started to question her purposes of being a police officer after her high school sweetheart, Bobby Prince, was arrested for the case's murder. And the one who managed to snap her out of her disillusionment was none other than the grumpy, irritable and cynical Frank Knight.
Case 32 starts out with Frank Knight buttering up the Player Character. As it turns out, his daughter's favorite book is being turned into a live-action movie, and she is a huge fan of the actress. Frank wants to get his daughter an autograph so that she'll speak to him again.
Case 44 of Pacific Bay (Case 100 overall) is a big one for Frank Knight. Chief Marquez is one of the suspects in the murder of Colonel Spangler and he becomes emotionally invested in the case. Much of the case has him wishing that Andrea is innocent and he even threatens to leave the police force if she's guilty. Keep in mind that Andrea singles out Frank for discipline more than anyone else so it shows just how much he really cares about her. He also asks the player to give him some privacy so he can have a private conversation with her after the real killer, Pearl Montana, is sentenced.
Amy and Russell's Big Damn Kiss at the end of Pacific Bay's Case 56.
How the team forgave Frank Knight for his crimes and attended his funeral.
In Case 9, a runaway named Benjamin Scott reveals that he left for Africa because he's embarrassed by his family back home. Upon hearing this, Elliot goes out of his way to look for the kid and tell him that his family loves him, and that he should be happy because Elliot himself wasn't so lucky when he was younger. This hints at Elliot's Hidden Heart of Gold, implying that his Jerkass personality is just a facade. When Benjamin reaches a reality crisis in Case 12, Elliot is the one to console him and convince him to go back to his parents.
When Ambassador Stern's son is traumatized by the events of Case #12, Lars befriends him and manages to help him feel better.
The end of the Eurasia arc has this adorable moment: Angela shows off her nesting doll of Jack, and Jack wonders why his doll is the smallest. Angela says it's cause he's the "baby" of the team (being the youngest field agent), and while Jack is confused, he thanks her for making him feel loved.
In Case 21, Jack's concern for Angela and Lars' well-being during their attempts to stop the plague is quite touching.
It's also sweet to see how dedicated Angela and Lars are to helping with the plague victims and trying to find a cure.
After the killer is arrested, Lars is still very sick and Jack refuses to leave his side until he knows he'll be okay. When Lars is shown to be alive and well after receiving the cure, Jack doesn't even listen to the joke he's making and immediately hugs him tight. Lars then thanks the player, saying he wouldn't have been cured without them.
Chief Ripley, deciding that the case had taken too much out of the team, sends them off to Bollywood for a much-needed break.
The appearance of Lars and Angela's children, which allows the Douglas family to finally spend some quality time together for the first time in a while.
Lars spends the entirety of the case reading the guru's book, convinced that he's doing something wrong by not being with his family all the time. Jack (disguised as the guru) tells him that he had been on the right path all along, since his job allowed him to bring justice to those who needed it. Lars feels better about himself afterwards, and tells the others that an individual he admired a lot helped him to see the light. What made it better was that he knew it was Jack all along.
In Case 23, Lars and Angela renew their wedding vows in the Tiger's nest monastery, while their kids watch. It's disgustingly adorable.
Also in Case 23, Marina forgives Jonah for shooting her in Moscow, and then asks him out.
In Case 27, Sanjay returns in perfect health and looking pretty happy after we lost track of him in Case 24.
Sanjay's arc was finally resolved in Case 30, where Carmen officially became his legal guardian.
In the same case, Chieko gets some closure when the player finds Hiroshi's locket, and tells her that despite SOMBRA's efforts, Hiroshi never forgot her. Angela then helps her find an adopted family, to Chieko's delight.
There's also SILVERee helping the player find the brainwashed children's memories, as atonement for his part in SOMBRA's scheme.
In Case 32, the entire team pulls together to rescue a kidnapped Elliot, with Jonah pulling a Big Damn Heroes to disarm the kidnapper and Carmen fussing over Elliot once the kidnapper is down. It's also heavily implied theplayer gave the kidnapper a Death Glare for daring to hurt Elliot before cuffing them and hauling them off while Carmen tends to Elliot.
It's also kind of sweet how Elliot tries to downplay his injuries so Carmen won't work herself up. It doesn't work but points for trying.
At the start of Case 38, Jack calls the Bureau team a family, and says he knows in his heart that nobody within the team is a traitor.
In the AI, when the possibility comes up about Carmen being the mole, Elliot fiercely denies it, showing how much he cares for her as a Parental Substitute.
Case 39's AI expands on Marina and Jonah's relationship, with Marina admitting that she cares for Jonah more than she'd realized and Jonah's half-sister Lily revealing that since Jonah joined the Bureau, all he told her about was his fondness for Marina.
For a case that was meant to reveal the identity of the Bureau mole, Case 42 has several moments where the family aspect of the Bureau shines through.
When Jonah finds out that Jack's gun was used to kill Lavinia, he looks saddened by it, then declares that Jack can't be the mole. Considering their usual dynamic, it's sweet that Jonah would still stick up for Jack in this situation. He also is the only one who deduces that Carmen could be in danger in Chapter 3, and saves her from the assassin who the mole had sent at the beginning of the district.
When Elliot is flagged as a suspect, he locks himself up in the library and refuses to talk, leading to Dupont to tell the others how concerned he is for him.