Something you aren't realizing is that retail brick and mortar pricing "market" value is completely different than online auction pricing.
We sell Zelda III for $19.99 and Super Mario World for $17.99 and Super Mario All-Stars for $24.99.
I can't get that on ebay for those all the time and with our high sales tax those come out to be much higher than ebay, but they are competitive and we sell them. All the time.
Yes, that is what makes our money, but again, your whole idea for this post was to complain about classic game stores and the main reasoning was that you can't get deals at them. You can. Like any place. You just have to "look" for them. If they have Mario for $45 but boxed Super Turrican 2 for $5, you obviously have a deal there. Most game stores don't bother with unpopular game pricing unless they are run by collectors or are corporate and keep up with value.