I personally use Wordpress with Foxycart.
Some things to think about are: do you need to keep track of inventory with this system? Do you need to display to the user how much product you have available? Do you need to take coupons? Issue gift certificates? Calculate shipping for a wide variety of package sizes and products? Offer multiple shipping methods? Offer sales to multiple countries? Deal with multiple currencies? Allow backorders? Set something as out of stock? What kind of sales reports are you looking for from the system?
