The fact that Billy sees Doctor Wernicke as a father figure, and supposedly keeps him alive with nanomachines.
Early in the game (when you first find the group of inmates gathered in the solitary confinement area, after being drug 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 might saved your life in an insane asylum could be considered heartwarming.
In Whistleblower when in the attic and getting chased around by Dennis who wants to send you to "The Groom" a heavily deformed inmate startles you as you squeeze between a bookshelf to warn you about staying quiet and that if caught, you will be sent down to Gluskin. The inmate then leaves but he seemed very concerned for Waylon's safety. The same inmate later shows up just in the nick of time to save the now captured Waylon from getting his genitals shredded off by Gluskin.
Reading Waylon's notes about his family shows how much he really cares for them.
One document reveals that Billy willingly agreed to being experimented on in return for the promise they'd pay and support his mother. It also reveals she already died without his knowledge, and that they might have had a hand in it.