Here are the things I like about my FLGS and some of the other gaming stores I have been to recently.
1.) DISCOUNTS: My FLGS (Mind Gmaes in Toledo, OH) gives me a 20% discount on everything because of my frequent shopping. They send out cards worth 10% to all of their customers several times a year (which I can use on top of my normal discount). Games Workshop product is always discounted 20% (and not just for me). Older product (that is moving poorly) gets even bigger discounts, with still bigger discounts promised for teh enar future.
2.) D20 COMPLETENESS: My FLGS stocks just about every (print) D20 product that passes through the major distributors. You don't have to buy a lot of everything, but you need to get at least one of everything (more if you've got a lunatic like me buying it all up as soon as it becomes available). Note that this does not mean that you have to go out and buy up all of that backstock, as that would be far too much of an investment, for a product that sells best (at least to my way of thinking) when it is brand new.
3.) RPG VARIETY: In addition to carrying all of the D20 product out there, you've got to stock the other lines. Non-D20 White Wolf stuff (WoD, Exalted), GURPS, Palladium, Hero System, Savage Tales, Shadowrun, and Fireborn to name a few. The list really goes on and on. If you have to limit your selection initially, I think the non-D20 White Wolf stuff is a must-stock line.
4.) MINIATURES (and lots of them): You really need to carry the Games Workshop stuff, though I think they demand that you keep a complete backstock (which might be kind of pricy starting out). Warmachine seems to be a big seller currently too (I'd also keep the non-Warmachine/Iron Kingdoms miniatures). Reaper is probably a safe bet too, though their Dark Heaven and Warlord lines will probably move better than their Exalted or L5R lines. Confrontation is popular and difficult for a lot of stores to stock; if you could do so, I bet it would sell well. Some items that I am into currently that probably don't have a lot of amss appeal are the Wargods of Aegyptus miniatures and RAFM's CoC modern miniatures. At this point, finances probably dictate stocking the WOTC D&D and Star Wars minis as well as the clicky games from WizKids. For the collectible minis, I would keep singles in addition to new boxes.
5.) USED PRODUCT/OOP PRODUCT (and at discounted prices): My FLGS doesn't presently stock used and out of print product, but some of my past favorite stores have. This applies most to RPGs and CCGs
6.) CCG'S: I'm not a big fan of CCGs and it'll probably show here. I think you would be well advised to stock Magic: The Gathering and one or two other card games that are hot at any given time. Right now that would probably be Versus and maybe Wars. I wouldn't order anything except Magic (and maybe not even it) in large quantities.
7.) BOARD GAMES: I would stock the abstract/German board games, especially Settlers of Catan and its expansions/derivatives. Risk (and its derivatives) are also probably viable.
8.) DICE: Have a good selection, but don't go overboard.
9.) OTHER GAMING STUFF: Some mats (markable and felt) and dry erase markers are always nice. I'd try to have a few pieces of terrain that goes specifically with the felt mats. The Army Transport miniature cases seem popular now too. I wouldn't go overboard with any of this stuff though.
10.) GAMING SPACE: Large. Comfortable. Separate from shopping space. A store I was in just this weekend had incredible play space. It reminded me something of a mix between a rowdy fantasy inn and a frat house. It really made me want to sit down and play and get to know everyone there.
11.) A STORE CAT: My girlfriend/fiance loves cats.
12.) A BULLETIN BOARD/ORGANIZED GAMING: You have to have a place to announce what is going on at your store, and you have to have stuff going on at your store. You should have RPGA gaming, Magic tournaments, D&D/Star Wars mini tournaments, clicky tournaments. The bulletin board should also provide space for players seeking players whether they take advantage of your gaming space or meet in a private residence. YOU DO NOT WANT AN EMPLOYEE THAT IS PARTICULARLY EXCLUSIVE WHEN IT COMES TO A GAME ORGANIZED GAMING. If it's his private group or whatever, fine, but he should not be able to exclude people from RPGA or other organized events. I have been known to divert my considerable gaming allowance from a store for wronging me in this way; and I spend a lot on gaming. Enough ranting.
I think that's it for now. Good luck to you.
Chad