Justin Tadlock publishes a helpful post on his new venture for theme reviews on why you should prefix everything. I guess it is time for a refresh after Nacin's 2010 post on the subject that has been referenced many, many times. Also, his exceptions at the end are quite worthwhile, especially on third party scripts. Handle names using prefixes means duplicate loads, and that stinks, so I'm really glad he made that exception.
Related, they are now recommended by StudioPress and Envato (and me too!) for theme reviews. Justin and Emil are top notch.