SEO Friendly Platforms are often overlooked, but they are a MUST!
This is probably the main problem that I have run into, it is so important that the application running a shopping cart, or content management system is complient with the search engines.
Zen Cart Looks promising
Drupal - Content management system (what my site is running on)
OsCommerce - Very customizable shopping cart that allows for rewrite of URL's to make them search engine friendly. This feature is an absolute must! Not only is it easier and more friendly for your shoppers, it helps the search engine spiders read your entire site and not get stuck or turned away by the code.