There are already quite a few good stores out there but keeping in mind the economy isn't great right now....
Stock, if it's listed on your site then stock it. If it's discontinued or you're not bringing it in any more then for gods sake take it off the site. Too many places leave old products up on their site even though they have no intention of restocking that item.
Prices, with the number of online stores we have a large variety to choose from so in many cases price is the deciding factor.
Shipping, free or low shipping costs affect the total cost of course so always a factor. Also, ship out as quickly as possible.
Customer service, I've generally had good experiences but there have been a few times where the owner/worker has been an ass and they lose my business forever. I'm not saying the customer is always right but at least try to come to some sort of compromise/agreement. Don't blow the customer off and say it's automatically their fault. I'll pay more at a store with good customer service.