Looking at a semi-business point of view, and only with the stores as such:
EB stores would need to charge a higher price on pretty much anything they can. Why? They mainly sell games and game related items, most of which you can usually get for 1/3 of the price (and sometimes better quality) elsewhere(internet.) Their revenue for sales is only from games, and that's what they're limited to.
Looking at JB Hi-Fi, they're pretty much an electronics retailer, excluding whitegoods and home appliances. Their revenue comes from TV's, DVD/Blu-Ray players, CD's, DVD's/Blu-Ray's, games, consoles, accessories. They also have a better buying power than EB.
TL;DR: JB has more money, and doesn't need to heavily rely on game profits, unlike EB.
fred, they probably have a policy/sequence when buying used games, check condition and if it's real or fake, polish the heck out of it, sell for an unfair price. Also, depending on the quality of the machine, it could make the Discs even more brittle/prone to damage.
All from a business standpoint(or a consumer standpoint), bigger stores usually sell the things you want for cheaper, but with the growing of the market into the internet, best to check there/here first.