Actually, the X.99 thing comes from
the good old days of mechanical cash registers, and not, as many think, from
the fevered mind of a marketing exec. The
promotional spin is just added value.
Let me explain: once upon a time, security measures in stores were not what they are today, what with CCTV cameras and computerised cash registers. One could do the sums of a purchase in one's head, and then pocket the payment without opening the till, and no one would ever be the wiser.
If, however, the price was an awkward number, which required one to give change from the frequently used coins/notes, the sales clerk would be more likely to have to open the register and get the small coins from there - at which point a record of the transaction was created.