I think the stores don't understand what a "collector's item" really is. With many stores they base their prices on popularity and demand rather than actual collectability. If you look at some of the games you see at Funco and other such places, you'll notice many of the popular games like Zelda, Zelda II, Contra, and such are priced higher than say a Captain Comic or a Dragon Power. The demand for these games is higher so the companies try and price accordingly. While that doesn't explain some pricing on carts, that's pretty much the reason.
Now other stores who want to sell these games either follow the same rule or just go what they think will be hot sellers and will crank up the price. Sometimes this mentality backfires: see Electronics Boutique. They got NES games and were selling SMB/Duck hunt for $11.99. Sure it's popular, but the pricing brass doesn't do the research to remember that EVERYONE got this game originally.