Originally Posted by DjSap

Best commercial one: X-Cart
Best open source one: Zen Cart

The most popular cart is OsCommerce, however the code is crappy as hell and it has tons of security leaks so don't touch that.

I would probably pick x-cart and get a designer/coder to modify it look like the shopping cart was custom built for the company, there are too many sites out there that look like each other which makes them lose credibility. If you need help in that area feel free to contact me.