I think it makes sense to charge a little over the online price, because anyone can get stuff online whenever they want, but there's a certain degree of novelty in finding something "in the wild." And you don't have to pay for shipping. But you could argue the opposite too: it's more convenient to go online to get what I want, and I can pick from everything available online, so I know I'm getting my game in the condition I want. And since it's less convenient to wait for my local store to get a given game in, they shouldn't charge as much.
At the end of the day, it's up to each collector to decide how much is too much to pay. Snatcher might be fetching upwards of $500 online, but there's no way in hell I'll be paying that much for it.