I recently ordered used from gamestop.com, only because of the b1g1 deal they ran. I'd never order from them again unless its a good enough deal like that for me to put up with the aggrvation.
No in-store return sucks big time. If they generally gave games in good shape, or always included manuals, it wouldn't be a problem. One of the games I ordered looked like the previous owner was Wolverine. Deep gouges on the top through to the data foil. Though they are paying for return shipping through fedex 2-day. The second game was encrusted with some kind of white stuff, toothpaste maybe, on the top and edges. Though once I cleaned it off it played fine, no scratches, though it didn't come with a manual.
AND GS overcharged my credit card, but CS immediately credited my card when I called, no hassle.
EB has in-store return, so if theres a problem, or if you want a manual or case, you can do that. Most of the used games I've ordered from EB were fine, some had a few scratches, but none were attacked by Wolverine, and none were covered in white shit. Though both stores love to put a ton of stickers on the damn case, EB seems to do that more, though my GS games had their price tags on top of EB stickers.
Prices are typicly similar. Price being equal, I would do EB. GS is running 25% off used temporarily, EB has that permanantly, plus they're doing a b2g1 deal for used.
In short:
Gamestop.com sucks.
Ebgames.com sucks a little less.