Penny guides are guides which have been on the market for a while and the publisher(or store chain) decide that the remaining stock of these guides have little to no chance of selling, so they issue an order to pull them from the shelves and destroy them. At that time, they are also marked as .01 in their inventory system, except in the case of BBV, which marks them .01 only AFTER pulling them.
Most stores have an agreement with the publisher that states that if they destroy the remaining stock of those items, they will receive a credit for their value from the publisher. This is why many stores are usually annoyed when we CAGs come in and buy the guides AT the penny price, since otherwise they would've received a full credit for those items.