In one of the Fortress of Solitude raids, Krypto is mind-controlled by Brainiac to attack. When the control is broken and Brainiac's forces are defeated, Lex calls it an "insane mutt" but Superman retorts that "maybe one day you will understand loyalty, human or animal".
The Booster Gold exploration tours are full of jokes and grandstanding on Booster's behalf, all spoken in a very cheerful and cocky manner. When he gets to Leslie Thompkin's free clinic in Gotham, however, he speaks very seriously and sullenly out of respect for the clinic, noting that "This Booster Gold endorsement comes free of charge".
Near the Crime Alley kiosk in Gotham you can visit the spot where Bruce Wayne's parents were murdered. There laying on the ground is a bouquet of roses undoubtedly left by their son.
In some of the higher leveled villain quests, Calculator seems to be more genuine in rooting for you and/or wishing you success.
This troper recently found that you can stop certain citizens from committing suicide. Let that sink in for a second.