Start with the basics: have quality content wrapped up in a professional package. Faint photocopies, titled registration, messy binding: all of these things will make a buyer think twice about carrying your book and not in the good way. Even a self-produced book can look polished without costing you an arm and a leg.
Have an ISBN number and bar code on your back cover. This is generally a requirement for national distribution and optional for local and small press, but consider adding it even if national distribution is a few years or editions away. Many independent stores use scanners in some capacity, and even if it's just to track inventory, having it on your books to start will put you one step ahead of those without one.
Verify any content restrictions your local store might have. Not all books are going to be suitable for all stores, and don't take it personally if the theme of your book doesn't have a place in one of the shops you are targeting.
Know your pricing structure up front. If you've got a bar code on your book you probably know your suggested retail price, but you need to know what your wholesale price is as well. Be prepared to sell direct to stores at 50 percent of your retail price. Sometimes you can work a better deal if your store is willing to sell on consignment, but many prefer wholesale agreements for their simplicity.
Offer to do launch events or artist signings at the store and put serious effort into publicizing those events. Develop press releases for your local news outlets and help bring in business not only for your own product, but the store as well.