Sadly, I can't really say. There aren't many organized store fronts for this sort of thing on-line. Gamestop is one of the only ones with real organization or reach, and as you've already discovered, they're prices are terrible.
For this sort of thing, I've always turned to EBay. It is considerably more hit-and-miss, but that's the nature of auctions and private sellers. But as far as a more centralized store, I'm afraid I can't help you.
Most of the re-seller market for these kinds of things are local game stores/pawn shops and EBay. You could try Craigslist as well, but that is even more hit-and-miss.
If you don't already have one, I would recommend a Dreamcast, along with an arcade controller. The Dreamcast is a very good and solid system. And at the moment its after-market price is actually quite reasonable. A lot of the better titles for it can be had for not very much money. And it's even pirate-emulation friendly, if you're into that. It is also one of the retro systems that best supports modern displays, as it is possible to rig it up with a VGA box and run it at higher resolutions.
The one major drawback is the controller. The design of its original controller is a bit bad. The buttons go mushy far too quickly, and the analog stick is slippery and topped with hard plastic. If you replace the original controller with an arcade-style controller, it becomes a magnificent system that can entertain you for a very long time. I strongly recommend picking up a Dreamcast.