One thing that comes to mind is to thank person that reputated you: say it could be a button (right next to comments) "Thank You" or something of that nature and when clicked a small message (via PM) will be sent anonymously to whoever ... It could also be use to appologize for something you said for any negative rep (if any and if you wish to do so).
Wonder how do you guys feel about this ?

Thanks for reading.
RB