On Wikipedia, the article for psychological pricing (ending prices in -99 or similar) gives the following suggestion for why it is done, as opposed to the psychological aspect behind it.

Others have suggested that fractional pricing was first adopted as a control on employee theft. For cash transactions with a round price, there is a chance that a dishonest cashier will pocket the bill rather than record the sale. For cash transactions with an odd price, the cashier must make change for the customer. This generally means opening the cash register which creates a record of the sale in the register and reduces the risk of the cashier stealing from the store owner.

This is not cited or sourced, so I wonder if any studies have been performed on this? Is it actually harder to steal from the store with odd prices?