I don't think there's a best
what are you willing to spend? what kind of features do you need? there's a wide range of shit you can use for ecommerce, from the horrible paid stuff (x-cart) to the horrible free stuff (oscommerce) to the decent/borderline overwhelming free stuff (magento) to the "I'm just sellin shit out of my garage" stuff (wordpress + ecomm plugins)
edit: and this is pretty much all just php stuff, I don't even know where to start when it comes to other languages like ruby/rails, python, asp, cloldfusion and others
(I deal with x-cart for my day to day and more often than not making it do what we need it to do is an uphill battle because of the way it was programmed)
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