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My #1 choice is Prestashop. Although it doesn't have a lot of themes available, the default one can be modified. There are tons of paid addons for it, varying in degrees of usefulness. But overall, it's a great system and has served me well for years. Really good for SEO.
My second choice would be Wordpress with WP-Commerce. You'll have a lot more choices for plugins and themes if you go that way.
Anything but Joomla.. ugh
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