As a Moments subpage, all spoilers are unmarked as per policy. You Have Been Warned.

General

The trilogy coming to end can be this to diehard fans of the series. As rigid as the scheduling and launching has been, the game is widely regarded as one of the best, if not THE best, in the series, and having to wait a couple more years for another stings.
Some of the targets are genuinely friendly, good to their friends, loving towards their family members, or treat their staff kindly, show remorse over their past crimes. While the likes of the Partners are still unambiguously evil, a few of the targets are still likeable enough (Alexa Carlisle and Marcus Stuyvesant in particular) for the players to feel at least a tinge of regret at their spectacular passing. Even a few of the ICA agents (especially Jiao, their handler) in Berlin are Just Following Orders, and only die for pragmatic reasons (so 47 can send a message to the agency to back off). Only Carl Ingram, Agent Montgomery, Hush, and Imogen Royce are played to be wholly unsympathetic, and tend not to be well-liked, in-universe or out.

Dubai

If 47 sabotages the exhibit to distract Lucy Phillips, Marcus Stuyvesant will take the opportunity to reunite with his daughter Cornelia. After getting over the shock of seeing her father back from the dead, Cornelia calls Marcus out on faking his death and putting her through so much grief as Marcus tries to explain his Providence connections and that he’s in danger. Before leaving, he tells Cornelia that she’ll have to have to accept him as dead, tells her he loves her and tearfully hugs her goodbye.

As cold-hearted as Alexa Carlisle is, she will break down in tears if 47 reveals that her brother Montgomery, who she murdered decades ago, loved her and was ready to let her take over as head of the family, meaning her murder of him was unnecessary. When Alexa then leaves to the balcony, she climbs over and lets herself fall to her death.
A low level one is the maid, Rosie, who was seduced by Patrick Carlisle and found out that he only wanted a one night stand. She's both humiliated, longing, and worried about losing her job in a very realistic scene that happens a lot with people of differing levels of class privilege.
While by and large an unlikable Bad Boss and murderess, Emma Carlisle can be seen holding and sombrely looking over Montgomery’s photo.
Lucas Grey's death, as he shoots himself to prevent 47 from blowing his cover. Even if he was ruthless and manipulative, he was undyingly loyal to 47, the closest thing 47 had to family and it’s clear from their interactions that the two trusted and cared about each other. Now that he's gone, 47 lost the only man in the world who truly understood him.

47 pays tribute to his fallen brother by wearing Grey's duster coat.
- In the ending cutscene, however, 47 is seen wearing his signature suit. As it’s set immediately after the mission as he meets with Hall in a diner, he must have abandoned the coat at the club.
If you successfully kill all eleven agents, you score a bit of bonus dialogue from Jiao, their handler... in which she’s audibly seconds away from a breakdown.
Jiao: Expertly done, 47. Expertly fucking done.

Amoral and ruthless organisation they may be, some might feel a bit guilty over exposing the ICA after 47 and Diana had spent years working for them. After all the adversity they have been through in the previous games, watching them fall, especially by 47's hand, is bitterly ironic. An End of an Era indeed.
- One might wonder about the other handlers and agents in the ICA. While 47 is a lone wolf, Diana, who noticeably did not guide 47 on this contract, could have had friends in the Agency. What will become of them now that their identities have been exposed?
If left alone after being fired, Jeremy Bolt will throw himself over a railing.

If you reveal that Don Yates was behind the data leak that ended his wife Valentina's career, Valentina will shove Don over a balcony to his death. Conniving bastard he may be, but unlike the previous targets and NPCs who killed others without a hint of guilt, Valentina is horrified and genuinely remorseful over killing her husband.
Getting a sniper team to kill Tamara Vidal when she's right next to Diana. Diana, who's grown to see Vidal almost as a friend, is quite remorseful, and points out that she now understands why she's not supposed to get close.
Diana's betrayal of 47, even if faked, is painful to watch for anyone who cares about either character. She finally confronts him on him murdering her parents and tells him that she always saw him as a tool. 47 can only croak out an apology before he passes out.
In the Heartbreaker elusive target, should 47 kill one of the brides, the other would spend the rest of the mission sobbing on a bench over her lost fiancée.
- If 47 hands them Newcombe's notebook and gets them to leave Viñedo Yates, Michelle, who had been squeeing over how beautiful the villa is, will panic over running into a serial killer and say that they should have their wedding at Phoebe's uncle's farm.

47's hallucinations in the beginning of Untouchable. He wakes up in a black void, woken up by Diana's voice. She taunts him as he wanders through the darkness, coming across Novikov being crushed by stage lights, Grey in a casket, Soders on the operating table, and the Partners in front of the Milton-Fitzpatrick bank clock, eventually coming face to face with all his former targets.
- The final step in getting 47 to accept his past and wake from his nightmare is to relive his assassination of Diana's parents, with the player having to physically pull the trigger on the car bomb that killed them. What's more, a young Diana was present for their deaths, only narrowly avoiding joining them when she was hurled back by the force of the explosion.
If you take 47 using the memory serum on himself as a wilful decision, then he decides that living a slave is preferable to having free will but doing exactly what he was created to do despite it.

While in the militia’s cave, Grey may chime in that some of the soldiers are good people who want the same thing as him and 47 in a tone that suggests he regrets abandoning them.
The village's master key is hidden under an old picture of a teenaged Akka with Farah, the former far happier than what's seen of her in the mission. Akka's intel, alongside her treatment of Farah if she discovers Hsu's death, suggest that she would have eventually tried to dispose of her mentor.