As guys before me said both Magento and CS-Cart have multi-store function.
Other carts that can boast of this feature are PrestaShop, OpenCart, Mijoshop, Aceshop, JooCart. There may be some other but I am not sure about them.
However, Mijoshop, Aceshop and JooCart combine OpenCart and Joomla. So, they basically have OpenCart's multi-store.
I would suggest you to read this post
about platforms that support multi-store. It is very basic but it will give directions to start from.
From my personal experience I can say that I saw live Magento shop admin panel with more than 40 storefronts. To be honest it was extremely slow on the back end but I am not really sure that any other shopping cart will be able to handle this number of storefronts.