One of the first things you get to do is play hide-and-seek with Lady Emily should you choose, and this is right after she runs up and gives Corvo a gleeful Glomping like papa was back from work. This one moment helps sell how much of a Parental Substitute Corvo has been to the girl since her early childhood.
Finding a picture Emily drew of Corvo without his mask, the word 'Daddy' written over it.
When she sneaks into your room because she feels comfortable there.
Heck, just about anything with Emily and Corvo. Which makes the Low Chaos ending where she runs into your arms all the sweeter. The part where she buries you next to her mother more or less says she thinks of you as her father.
After rescuing her and bringing her back to the Hound Pits, Corvo will step off the boat, and offer Emily his hand to help her get back on land. Purely symbolic, but also purely adorable.
What's the first thing Corvo and Emily do when he finds her in the Golden Cat? She immediately rushes into his arms, and he picks her up and twirls her around.
Anton and Piero huddled under the tables after the betrayal of the Loyalists. The two of them are talking like old buddies and lamenting all the time they wasted being rivals.
It becomes a Crowning Moment of Awesome too when their combined knowledge is enough to cure the plague.
The sparing of Daud. After all of your horrific means of neutralizing others and/or killing, you can roleplay Corvo choosing to reclaim some of his humanity and cast aside revenge by sparing the life of his Empress's killer. Daud himself is moved by the action, and even the Outsider is briefly at a loss for words.
Possibly more heartwarming even if you've been doing a Pacifist Run. Though you've avoided killing anyone (directly) throughout the entire game, it's implied a possible motivation for sparing his targets is because Corvo wants to inflict Cruel Mercy via Fate Worse Than Death. Daud is the first and only target he can let live and have it be unambiguously considered benevolence.
Daud's entire speech to Corvo is this if Corvo has done a perfect Pacifist Run to this point, with Daud reflecting on all the things he himself has done — murdering for coin, with no care for who he was paid to kill — and the path that Corvo chose. That Corvo, too, was asked to kill — and always found another way, even after all he suffered at the hands of the people he was sent to murder. The absolute Crowner comes if Corvo sheathes his blade and steps back, silently granting Daud his life. Daud sounds almost awed, to the point that it's nearly a Tear Jerker.
Daud: And you choose mercy. Extraordinary.
And it becomes even more heartwarming when he tethers away when you spare him. it's then that you realise that he could have escaped at any time, but chose to stay and either die or be forgiven.
While some people might find Piero revolting for being a Peeping Tom, he's sincerely remorseful when confronted and admits to being desperately lonely. It makes it all the sweeter to discover that the Bifauxnen waitress at the pub wants to know if he's married.
Going through the Lady Boyle mission and not upsetting the party. Even after earning the "Well Mannered" achievement/trophy for doing it, not upsetting a good time for everyone else just feels right, sort of like doing Pacifist Runs of Deus Ex: Human Revolution even after going through the game.
After Havelock's betrayal, when you finally get back to the pub, you find one surviving loyalist, Cecilia, who at first is reluctant to trust Corvo. If you go back into the abandoned apartment after things quiet down, you'll find a note on the floor, stating that she made a run for it, thanking Corvo for giving her the courage to try and escape from the pub, and after this was all over, she'd do her best to find Corvo again.
One of the parts of a low chaos ending shows Samuel and Corvo hanging out at the hounds pit pub, even having returned to nobility, and the differences in their caste, Corvo still didn't shut out the only man who stayed with him when everyone else had cast him aside.
In the same ending if you saved Curnow then you get a scene of him and Callista reuniting.
The scene in Low Chaos playthrough, where you find in a warehouse an Overseer sick with the plague begging his friends to kill him before he loses him mind and becomes a weeper. After they decline at first, and one offers his share of elixir instead, they finally go through with it, killing the sick man as he's reciting the Seven Strictures. The whole scene is a very touching example of the selflessness that surfaces in the Low Chaos timeline, as people still have hope that things can get better. It's all the more touching when you realize that in High Chaos, the Overseer will claim that he's healthy, and his friends accuse him of trying to infect them all before they kill him.
A Pacifist Run in general is this, or even a playthrough where Corvo's only kills are his targets. Before the game even really starts, his life is destroyed: he's betrayed, convicted of his Empress' murder, tortured for six months, nearly executed, and generally put through hell — and then he's given incredible powers, and they make it so very easy to kill anyone and everyone in his path. He could do it without anyone suspecting a thing even as their fellows drop like flies... until Corvo eventually gets to them. But Corvo doesn't. He chooses to do what's right instead of what's easy. Despite everything he's suffered, despite all of the cruelty shown toward him, he rises above it and doesn't let any of it turn him into a monster.
Sparing Daud is made even more powerful if you don't even alert him and just pickpocket him. Look what he knows: All his men are absolutely loyal to him. So only one person could do it. Corvo, who have very good reason to hold a grudge. So, this one guy, who you expect to murder you on sight, got in without him or anyone else seeing him, to point where he could stab you. Yet, what he does? Just pickpockets you and leaves... once again, without anyone seeing him. Guy who you expect to kill you moment he sees you, just got in, got into position to kill you and decided not to do it.
In the Golden Cat, you can see two of the prostitutes quietly dancing, just holding each other close and slowly turning. No attention is drawn to it, but it is still quite a touching scene.
Also from the Golden Cat is a scene where a guard is telling another that he's fallen in love with one of the prostitutes, and that when he's saved enough he'll take her away from this life. Even though his friend is less than supportive, it's still nice to hear someone cares about the girls.
From Knife Of Dunwall, "Billie. I forgive you." The Outsider's reaction, where he reveals that Billie managed to get out of Dunwall and make a life for herself makes it even better.
"Daud, the man who murdered an empress.... the man who spared his betrayer's life.
Brigmore Witches reveals that Daud and Billie are still keeping in contact via letters.
For the non-lethal elimination of Timsh, you need to utilize a plot cooked up by a former noble that Timsh wrongfully disgraced. Part of that plan is to make Timsh's house smell like a Weeper den. Remarkably, although rotting bodies and plagued rats are in plentiful supply, the disgraced noble goes to great lengths to create the right stench without using plagued materials, out of concern for the guards and servants living in the Timsh estate. From what we see of Dunwall society, the Aristocrats are often criminally indifferent to the lower class, and a noble who has nothing to lose should be even more reckless than normal. Yet not only did he delay his plan and put himself at risk, he also relinquishes an OutsiderRune as payment to ensure that innocent bystanders won't be hurt.
It's doubly impressive if you remember that Outsider Runes compel most people who own them to become obsessively possessive. Willingly giving one away is not as easy as it sounds.
It's widely speculated that, Wallace, the Jerk Ass butler, told Cecelia "not to come outside, due to her not receiving any bonus" in an attempt to save her life knowing full well what was about to happen.
In a Low-Chaos run of The Brigmore Witches, if Corvo spared Daud in the main game, the last scene is Daud reverently laying his sword at the Empress's grave before leaving the city.
After taking care of Delilah, Daud receives a notification: Target Rescued: Emily.