In an odd way, the exchange between Percy and Brutal after Arlen's execution qualifies. As depressing as it is to spend your life working as an executioner, it's pretty damn heartwarming that Brutal still has enough heart to think of the prisoners under his charge as human beings, and that he actually cares enough about them to speak up when someone takes joy in killing them.
During John's execution Paul is willing to let John go without the hood because John is afraid of the dark.
The cops' friendship with John in general. They take him to see a movie, something he's always wanted to do, the day before his execution. And as John stands before the electric chair feeling the hatred from the parents of the girls he was accused of killing, Dean tells him to focus on how he and the others feel about him.
John getting in on The Mouseville hoax after saving Del's mouse.
John watching the "flicker show", seeing Fred Astaire and Ginger Rogers dancing cheek to cheek in Top Hat; even the nice symbolic touch of the camera slowly tightening on John's face, with the light from the film projector creating the illusion of heavenly rays behind his head.
John: Why, they's angels. Angels, just like up in Heaven.