The independent stores here are mostly rip off's, but if you search carefully you can get prices that are better than ebay especially on hard to find stuff like Sega Saturn games which are expensive to ship. However the shop that I am talking about here sticks all their good stuff on ebay leaving nothing in the store but old sports games and crappy games in general, you won't find any gem games or RPG's here.
Other times you can get stuff much cheaper on ebay, some guy offered to sell me After Burner for the NES for 10$ in cart-only, unknown working condition, at that point I just walked away from the Flea market. I am a female so some people there probably think I am really stupid and will pay any price for game x, especially when most of the vendors do not have things clearly price. The Flea is a mixed bag though, there is one shop at the back that does REALLY good and fair business, and their prices are reasonable and sometimes more than reasonable. They also don't take excessively scratched games in for trade and the prices are different for used, new, complete and incomplete games, so its very fair, and I do not think I have found a case when they charged more than ebay does. They treat their customers fairly whether it be woman, kids or people who look like hardcore gamers. The prices are stickered on the games so they don't just make up a price based on the customer like many fleamarket sellers. This shop stocks pretty much ANY kind of game you want, and does not ebay all the gem games leaving nothing but crap in stock hoping that someone will buy it. Their selection of newer games is bad though, but since I don't own any of the new 3 consoles, this doesn't affect me.
I really wish there was an independent here doing business in new release games, old games and everything inbetween. If there was I would support them over GS for sure, provided their prices were not inflated (although hey, aren't GS's prices inflated enough as it is?). I mostly shop on Amazon, Ebay (very carefully), half.com and any other site that is offering a deal.