I think a lot of people are going to have their own opinions here, just because there are so many options available, of course I have my own recommendation.
I would recommend Cubecart, it's a PHP / MySQL cart that's fairly simple to modify themes and templates for. It's not the fanciest cart out there, it's rough around the edges, but it's easy to work with. (
CubeCart - Free & Commercial Online Shopping Cart Solutions).
Or, depending on the complexity of the store, you could use Wordpress with a Shopping Cart plugin. There's literally countless Wordpress themes out there, which makes it easy to find a design that works, and then integrate a store into it.