There really arent many options for Joomla per se. The one thing you need to make very sure of is, do you really need a shopping cart solution that directly interacts with the Joomla userbase? Will the people you are selling to be writing articles and editing content, or are they simply signing up to purchase and maybe leave comments?
Are you needing the integration simply for theming and consistency? If it's just for themeing then it's generally pretty easy to insert the Joomla header/footer into a proper shopping cart systems theme such as Magento or any of the hundreds of other ones out there. That makes it easier to upgrade and patch as well.
Even with a bridge that Tess suggested, you typically still have to do a lot of theme work to the script you are bridging to make it look consistent. Using the Joomla wrapper is not a viable option.