Actually doesn't surprise me that some shops would do something so underhanded with the bad economy, then again it could all be the store manager that's doing it, who knows really. All those freeware companies need to team up and sue them out of business in a huge lawsuit, and some of those companies aren't so little and have deep pockets and could probably afford a long drawn out court battle.
So it's CCleaner, SpywareBlaster, ZoneAlarm, some Symantec software, etc., and the list just keeps going on and on.
I think you will find their story will be: a fee for time taken to gather the software, fee for time and materials used to produce the CD and cover, package it up, transport it to the sale point. Somewhere they will state that the software is "Freeware" and the price of $2.99 is only for the cost of providing the service.............a brokerage fee as such.
However I agree with all comments that is this practice is not only immoral, but stinks, lousy and a concentrated effort to boycott those shops partaking in this "lower than a snake belly" practice.
I will now be keeping my eyes open here in Aus, thankfully I have not seen this happening here (yet)