WP eCommerce by GetShopped is now fully integrated
WordPress 3.0 introduced the ability for plugin developers to build their own custom post types. This means that the main data is held in the same table as your WordPress posts and pages and therefore means that other core wordpress functions and thus other plugins can see them.
In the case of an eCommerce system, this would mean that all your products are now held in the same table as your posts and pages. One obvious advantage of this is that to search your site just became a whole lot easier!
I've just finished a large upgrade to WP-eCommerce website using GetShopped's latest 3.8 architecture with that integration into WordPress model - see rockwaterstudio.com. Along with a cosmetic face-lift it makes the site far more concise, easier to navigate and also better for Search Engines (SEO).