Forum Moderators: Robert Charlton & goodroi
1. urls with multiple parameters in a query string, or
2) duplicate urls that resolve to the same page
You can find many carts that don't create either of these problems -- even templated, third party hosted ecommerce solutions. Beyond that, I'd say look to the functionality that you need for your particular business. That should be the key factor.
Also, whatever you go with, plan well. Even the best tool can be used poorly - there's never a guarantee that any software can give you good ranking.