I personally don't have anything against Gamestop, but I rarely shop there since I can easily buy things cheaper or sell things for a better price elsewhere. Their pre-order bonuses have enticed me inside a few times, and it's always nice enough to browse, but it usually comes down to price for me. Generally, things are distinctly cheaper on eBay or Amazon even with the high shipping costs these days, and there's also no sales tax -- take that, local government!
However, I almost always buy things factory sealed. I keep most of the games/CDs/movies I buy, so I'm pretty picky about condition and it's somehow nicer to be the only owner of stuff that's in my collection. Of course, out-of-print stuff is an exception, so I take what I can get when it comes to that. Honestly, this forum is about the only place I buy used CDs -- both because a lot of this stuff is hard to find elsewhere, but also because most of the people here actually appreciate their CDs and don't treat them carelessly.
On the topic of retailers, my (perhaps mistaken) impression is that it works something like consignment. The game publishers send out their product to the stores, who then pay a share of the retail price back to the publishers once the item sells -- we'll say 50-50 as an example. So if you buy a $60 game, the retailer gets $30 and the publisher gets $30. If the retailer puts it on sale for $50, that missing $10 comes out of their share (unless the publisher is funding a promotion), but if the game permanently drops in price, they split the take again -- when it goes down to $40 they each get $20, etc. This is obviously way oversimplified and also ignores the possibility of distributors, but that's the general idea.
So the upshot is that as long as you buy the game new at retail, the publisher is getting something. But if you really want to help them out, you could try buying stuff at their company store. Most of the big publishers have online stores, and I think EA even offers free shipping. Or even better is buying stuff from their store digitally so they don't even have to spend money on packaging. Of course for my own part I don't feel bad in the least about buying stuff from the secondary market as long as it isn't stolen or bootlegged -- my money is usually helping individuals instead of large corporations that way. I don't begrudge the publishers money, but since somebody has already paid them for the item that I'm getting, it doesn't really hurt.
I am disturbed by all this digital distribution, though. If I buy a game or whatever and decide I don't like it or won't feel like experiencing it again, I darn well want the freedom to get rid of it and get some compensation back. More importantly, I like having something cool on my shelf that I can thumb through or take with me to a friend's house or whatever. This digital distribution thing gives much too little in return for its disadvantages. But since the publishers make way more money that way and people are willing to get sucked into it, digital distribution looks like it will keep getting more widespread. Meh.