Don't know about SEO, but it sure can affect your car.
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I will look at Magento, As far as the site we don't have any duplicate content. We are using oscommerce and just wanted a better cart.Depends on the type of website you're running. For example if you're running an e-commerce site selling physical goods and you are just copy and pasting the manufacturer's descriptions onto your store, then that is pretty much duplicate content everywhere on your site which doesn't help with SEO.
I think what you do with the site will affect your SEO more than the shopping cart. Most shopping cart now days are all pretty good with SEO.
I'm a big fan of Magento.
Almost all shopping carts are SEO optimized. Do research on the cart you plan on using and they should outline the SEO options available.
Don't know about SEO, but it sure can affect your car.