Magento is probably the most complete. It's also the most complicated to customize. If you don't have a firm grasp of MVC programming and the Zend Framework, good luck...
I am using Magento for some time now. Although right now I use it for single store, the transition to multi-store is easy. From my experience it is excellent platform. The customization options are infinite, but you can start with almost off-the-shelf solution. Cheers Sty
Magento has some excellent features although it can take up quite a bit of resources if not configured properly.