EDIT: Got to split this into two posts
Lots of good points from Constantine,
I've been an eye-rolling party to many a bad game store idea and a even a few good ones. Some points:
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Professionalism, professionalism, professionalism. This is a business - treat it like one! You seem to have that message down, but hammering it home cannot hurt in the least. You need clean, friendly employees. Once who are friendly without being pushovers, firm without being jerks, and knowledgeable without looking to rip off their employer (it happens). Difficult in the best of times and all the more so with a pool of gamers as your manpower stock. Of course to start out with you'll probably have a very small number of employees, or maybe it'll just be you alone. But hiring good quality people is vital. As SCD quoted elsewhere "First-rate men hire first-rate men. Second-rate men hire third-rate men".
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Organization. Make sure you're organized! Clutter encourages thieves, makes it impossible for folks to find what they're looking for and eats up valuable event space. A neat and tidy store (with clean bathrooms!) presents a professional, businesslike demeanour which only helps. As long as the staff are friendly, you'll still keep a warm atmosphere.
Having a good database allows you to track what you're buying and selling. It may not work for things like MTG singles (unless you're a GIANT operation),
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Hours. You find out what hours are good for your neighbourhood, but if you really need to save on labour costs (or you have no employees), closing on Mondays and Tuesdays is usually not too harmful to a game store.
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Deal-making. Don't cut 'friendly deals'. If someone is really confident or the customer is a very good one, special deals always seem appealing. In fairness, customers LOVE it when a store treats them 'special' because they're 'good customers' - it definitely breeds more spending and is a hell of a good way to breed loyalty. But you have to be very confident and sure of yourself (and your information) before you can do that, otherwise you'll just be taken advantage of more often than not.
I do not recommend special deals to anyone just getting started as that is some very dangerous ground to tread. Instead, if you want to offer discounts for good customers, work out your profit margins on various product and then publicly post a discounted rate chart. So when someone tries to argue for a deal when they're buying more stuff, you can point to the posted rules that state, sure you can get 10% off that Warhammer order - if it's above $250 (not an actual suggested discount rate - just a random example). Staggered discounts of 5%, 10%, and maybe even 15% (depending on the product) with appropriate price thresholds are a good start.
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Pricing. This is a sore spot and require a LOT of labour to get right but can really make or break you. You will need to provide a price point that is sort-of competitive with online stores without actually trying to beat them outright. That's the reality of gaming today. Too high and everyone will gripe and you'll be stuck with a lot of sunk inventory costs, too low and well... this will be a short-lived enterprise.
You'll need to feel your local scene out to see what the market will bear (not "how much can I get away with charging", but actually what is sustainable). Pricing - especially for items with frequent price fluctuations, like Magic singles - is a full time job (literally), but having single sales with GOOD pricing can really go a long way to solidify your customer base and providing a decent additional profit trickle.
You may not want to go into single sales until you're confident about the regular business (maybe a couple of months in?), but definitely keep the option open. Buying collections can net you a good amount of profit (since people selling collections typically take a loss on their overall value, in exchange for getting a lump sum of money and avoiding the work of sorting and pricing their stuff) or it can waste a lot of your money if someone unloads their junk on you, so it's another reason to really be aware of what everything is worth at all times. With the razor-thin margins in the game industry, good price knowledge can really make or break a store that right on the edge.
For pricing resources, you'll need to look at three things: 1) The local community. Things slightly change in value regionally and you'll need to take the feeling of the local market in mind. This one is the least reliable (as you're doing it by 'feel'), so it should have the least weight. 2) Major retailers. See what the big boys are charging. Usually they occupy the high end of the 'sensible' price range. For example, for MTG singles, starcitygames.com is a good 'evil behemoth' retailer, with easy-to-consult online pricing. 3) Online aggregates. Or more simply 'ebay prices' (or other auction or community-based sites with high numbers of transactions). End prices on ebay auctions give you a good idea of what's the price floor for an item.
The best part about doing this is when some dipshit tries to call you on price and you can point out that you are in fact competitive with both auction/trade sites and the behemoths.