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.