Not every store does ".99". The companies that charge ".99" or similar are trying to hook you in on a good deal, while the others that round it naturally are trying to hook you in on a good quality product. Since most consumer products are just pointless (shiny!) crap I think we see more of the ".99" used. :)
Some stores use the cent portion to encode extra information: 0.87 indicates a clearance item, 0.55 indicates a refurbished item, 0.20 indicates a damaged item, and so on.
