I have found a variety of ecommerce software available online for sale.
I think it first depends on the size of your business, what kind of experience you have with ecommerce software (e.g. are you technically savvy), what are your needs as a merchant (what kind of functionality is most important to you?). In addition to this, your solution should fit your customer experience because let's face it, if you don't have customers, you can't sell!
I would say CoreCommerce and 3dCart are solutions with top notch customer service. I also found a great resource to search for ecommerce software and purchase the best ecommerce software [zippycart.com] the site categorizes its ecommerce software for easier purchasing. Best of luck!