Well if you need a eCommerce website then there are several things you need to finalize, and a few things are:
1) whether you need a different look and feel for each category of your products?
2) whether you want each category/store to have different email, shipping, tax and payment gateway details?
3) Whether you need different domains for each category or store?
Basing on the above aspects you can go for joomla with virtuemart in it, or wordpress with wpcommerce OR the best option is magento. Magento will cover all the above mentioned features!
But if you need something simple then joomla is your best bet, combined with virtuemart it does provide a good ecommerce website but won’t give you the multiple store or multiple website features!
All the above listed open source applications are free and are very much search engine friendly, if you need a experts advice on which solution to pick then get in touch with us at: firstname.lastname@example.org , we are expert magento developers!