we are an running an online stores chain and for that we are using bit cart shopping store front which is very seo friendly as it's very easy to manage. i'll recommend you bit-cart.com
you can also try its starter hosted version for Free.
Magneto is undoubtedly SEO-friendly but there is some stuff that will help you to optimize Magneto SEO.
first, get the most recent release, 1.2.1. then, to get started, enable Server URL rewrites. You will find this setting under System => Configuration => Web => Search Engines Optimization. Another good thing to configure now you are on this screen is "Add store Code to Urls" under "Url Options". In most cases it is better to set this functionality to "No".
Indeed, Zen Cart may be a great solution for you in this case. Zen Cart is an outstanding open source system for online store management. It is a PHP-based structure that uses MySQL database and certain HTML components.
This system encounters several languages and supports different types of currency, which are available for free under the GNU General Public License.
Zen Cart evolved from osCommerce as a separate project, but unlike it, Zen Cart supports template custom design. One can always change a ready made design into a new one.
The variety of Zen Cart templates allows you to have the most unique and outstanding store on the net. And yes, it is SEO-friendly :)
I assume that most of decent carts today are optimized for search engines. I would suggest you to use LiveCart because it not only able to sell physical product but also support selling virtual item such as e-book.
Storefront is a good investement if you need too much of your shopping cart service ... However, if you sit down and go through thousands of options you can consider simpler and probably less expensive solution is not the time.