One of my favorite "unique punishment stories is "Cage of Brass" by Samuel R. Delany...in which "getting better" is the punishment.  Essentially, the central character was convicted of a crime and placed in a life support vat but with full sensory deprivation.  He essentially went crazy and that was the punishment, if he did anything to harm himself, the life support system would simply kick in and fix him.  In the logic of this story, mind-numbingly boring immortality was the punishment, as it led to a kind of self-aware insanity.  Basically it was a story looking at the psychological and emotional implications of extended solitary confinement.  That's an idea that hasn't really been pursued very much, and some element of that is likely to work in what you're interested in.  I guess, the main question is: what element of the plot is best served by a non-typical punishment?  Because I have my doubts about the whole crime/punishment thing, I'm always interested in how the two things don't really match.  I mean, what if a person is innocent and there's a flaw in the system?  That question has served me in all 1 or 2 crime/punishment stories I've written, but again, it all boils down to what you want to say and what best helps you say it.