The fact that Billy sees Doctor Wernicke as a father figure, and supposedly keeps him alive with nanomachines.
Early in the original game (when you first find the group of inmates gathered in the solitary confinement area, after being drugged and left there by the priest) there's a psycho inmate locked in a cell trying to get out, with his arms past the bars, grabbing at air. Next to him is an escaped inmate sitting in a chair. Upon nearing the inmates, the one in the chair jumps up and starts trying to strangle you. He suddenly stops because the guy in the cell has grabbed him by the head, and is then pushed off the balcony. The fact that one of the inmates actually saved your life in an insane asylum could be considered heartwarming.
Miles realizes this at some point during the story, and that's why he shows pity for him when the Walrider kills him.
"I hear him muttering about security protocols, containment. What if he's not the problem? What if he's trying to fix it?"
"You've escaped one Hell, Chris Walker. God help me, but I somehow hope you didn't find another."
In a similar vein, Waylon consistently maintains empathy towards the other patients of the asylum, even Eddie Gluskin, the guy who tried to castrate him with a buzzsaw. The guy has an impressively big heart.
"This man thinks he's in love. He thinks the therapy made him better."
At the end of Whistleblower, Jeremy is on the verge of stabbing Waylon to death to keep him quiet about Murkoff when the Walrider swoops in and completely eviscerates him from the inside out. Once outside, Waylon hobbles into Miles' car that he left at the gate in the beginning of the first game, and he looks up to see a figure of a man surrounded by dark smoke. He doesn't take his eyes off you, and before the panicking Waylon can do anything, he summons up a dust storm that blows the gate open, allowing Waylon to escape with evidence of Murkoff's corruption. Miles, you absolute legend.
The Twins letting Miles go without chasing him anymore after Father Martin's death. This could be interpreted as them paying their final respects to Martin, which, coming from a couple of insane cannibalistic murderers, is saying a lot.