I still go to GameStop from time to time, and also Best Buy which has decent prices for used games if they actually have what you want in stock (but having good prices typically means people buy up anything quickly). The quality of GameStop's stuff has really gone downhill recently, finding games with cases and manuals is getting more and more rare, as well as the disc or game card itself being in good condition. Not to mention the huge stickers with very sticky goop they slap onto everything, and their prices aren't as good as they once were. I can still find deals there sometimes though. Best Buy has higher quality standards for used games.
But yeah, it's mostly eBay now since there are so few other options these days.
I'm not in a rush because I have plenty to play at the moment, but I plan on eventually purchasing some DS games.
The advantage of buying in-store would be that you could check out the quality of the item before you buy, such as if it contains its case and manual. Their online stock is typically the copies that didn't sell in store, which means you're highly likely to receive just the game itself and absolutely nothing else. And if it's a disc, it'll likely be one that was resurfaced due to being returned as not working. If you don't care about having a case or manual, then you can buy online.
Be warned however that GameStop does not check if a game is counterfeit, so be sure to closely inspect anything you buy if you want it to be legit. You can return online purchases to any store.
What about eBay? I've only made a few purchases on there and nothing recently. Are there bargains? Do I need to be regularly monitoring the site to get them? Or should I just wait until I want to make the purchase?
With eBay, the best deals tend to come from auctions so you'll want to wait for those to pop up and follow them. Sometimes, a game will have a good price as a Buy It Now, but of course anything with a good price will be bought up quickly, so you'll need to check the new listings often to get that kind of a deal. You can use the search feature to look over completed listings and see what prices games have sold for (or didn't sell) in the past few months. Newer sellers with less or no feedback get less attention, so you can usually get better deals buying that stuff though it is also a little more risky since the buyer is relatively unknown. But eBay has plenty of protection policies, so you should be able to resolve any problem that happens. It would just take up some time.
Also of note, I'd suggest to not buy anything that ships from outside of the US, including Canada, but especially Hong Kong. Anything from Hong Kong
is counterfeit, and there are even counterfeiters selling from Canada. It probably wouldn't be a good idea to bid on anything without pictures, and be certain to inspect anything you do buy to make sure it isn't counterfeit. There are a lot of fakes out there, and even if they do work, they are much lower quality than originals, and using them in a 3DS voids the warranty.