Corvo, I am very sad. They say that you are dead like Mother, but I'm going to put this note in a bottle and throw it into the river because I do not believe them. Living here is very strange. I do not like it, so please come for me if you can.
Not to mention the pose Corvo finds Emily in - caught in the act by the Pendleton twins.
The Heart makes an observation about Callista, who is teaching Emily how to be a lady.
She dreams of freedom, and the decks of whaling ships fast after the beasts of sea. But alas, she is a woman.
If you go to Callista's room in the tower while Emily is in there, you get to see her as a traumatized child.
In the sewers after you break out of prison, there are two plague corpses off to one side, hugging each other, with a journal that indicates that they couldn't afford enough elixir, and decided to just wait it out in each other's arms, hoping their fire would keep the rats away.
Both High Chaos endings. If you spared him, Samuel is swept away by a giant wave. If you didn't, Corvo spends a quiet - possibly remorseful - moment at his graveside. Emily and Corvo cannot prevent Dunwall's ruination - if Emily survived. Her death only speeds Dunwall's complete and total collapse.
Daud's speech to Corvo when Corvo confronts him in a Low Chaos Pacifist Run, culminating in Daud's words to Corvo if Corvo sheathes his weapons and steps back, silently granting Daud his life. Daud's almost awed tone just makes it all the more powerful.
Daud: And you choose mercy. Extraordinary... Unexpected.
Let that last word sink in just a little bit. He fully expected Corvo to kill him for his crimes.
More than half of The Heart's lines fall under this heading, especially when the sheer misery of the setting's inhabitants begins filtering through. In these lines, almost every single unnamed NPC ends up getting painted as The Woobie: male survivors have lost everything to the flood and the plague, are forced to perform backbreaking work that their superiors will never be satisfied with and driven to steal from their fellow workers just to get by; female survivors have to starve themselves just to make sure their children are fed, and are often driven to alcoholism; the servants are horribly mistreated, deep in debt, worried that the other servants don't like them, and likely to be killed by weepers; the prostitutes are little more than slaves, taken from broken homes, shipped into the Golden Cat under the belief that they'd be working in a factory, terrorized by the Madame and in danger of catching the plague from their clients... even brutal enemies like the members of the Bottle Street Gang and the City Watch have a few lines that make them genuinely pitiable. Most saddening of all is the fact that many NPCs are revealed to be contemplating suicide in some way - and for good reason.
At some point in the game, you find two male survivors, obviously close friends. One is slowly dying in the other's arms (the other is also dying but at an earlier stage), being dragged out of the mound of corpses that the city watch are dumping in the Flooded District. The dying man genuinely thinks he's being brought to a hospital and the City Watch will help him, promising to 'do things right' when he gets better. His blind optimism is heartbreaking considering the Foregone Conclusion, and his friend trying to let him down gently doesn't help.
In Knife Of Dunwall Billie Lurk's death in Low Chaos is an absolute heart-breaker. She smiles at him. Daud actually holds her hand.
If you thought Daud deserved his fate at the end of the main game, your opinion will be changed after playing Brigmore Witches on Low Chaos. Almost every momment during the lengthy ending is a tear jerker for Daud.