Really comes down to how much you want to pay for an off the shelf solution or how much time you have to develop with something like zencart or oscommerce.
I have been developing with volusion
Shopping Cart Software by Volusion Ecommerce Solutions, product cart
Shopping cart software: ProductCart by Early Impact, zencart, oscommerce or completely custom based on need. It really comes down to time, money, customization, if you want free software updates for bugs/new functionality, pre-built admins (CMS), etc.