Mr Freeze had his own character arc over the course of the series. After his wife was cured and married her doctor, Victor had nothing left and wanted everyone to feel his pain (in Cold Comfort he did nothing but screw people over by taking away things they held most personal and dear) He's whole motif was "revenge" and in his TNBA episode it was revenge against the world, rather than 2 or three people. Bruce doesn't trust him in Batman Beyond's Meltdown (VERY good episode, I recommend it) because of the whole revenge theme and the fact the Bruce has been through this whole villain reformation thing before with Riddler, Ivy, Harley, Penguin (to an extent), etc...Arnold Wesker is the only one out of Batman's rougues who actually seriously went sane.
Clayface, was always kind of a jerk even as Matt Hagen if I remember right. He probably was stealing in Holiday Knights for a cure. Growing Pains he was just trying to get a piece of him back that went missing...He was in Justice League not really wanting to join Grodd's Secret Society if I remember correctly.