Prices are first set by collectors at the wholesale level. This pricing is based on how rare they are, how hard they are to catch, and probably a zillion other factors.
Then, LFSes purchase them from wholesalers and mark up the price to accomodate shipping expenses and the store's overhead.
Finally, the price might be further adjusted based on the market. For example, Ocellaris clowns were much more expensive (at least in my area) after the release of Finding Nemo.