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I've also have done sites with joomla running the main site and the "store" in a subfolder or subdomain with similar template design and running my chosen (commercial) ecommerce cart system.
But the integrated Joomla ecommerce offerings (3rd party components) are rather lame, IMO. The only real player is VirtueMart but thing I notice is they tend to stay compatible with 1-2 versions BEHIND the latest Joomla version. That's not something I'm willing to risk with a full blown ecommerce store. I prefer to stay up to date for security reasons.
If you need to list a handful of items say for a small club or something, sure you can find some ecommerce add-on that should work fine. But for full blown ecommerce I want well maintained, often updated, quickly patched, PCI compliant and payment gateway vetted ecommerce package.
[edited by: T_Miller at 1:27 am (utc) on Mar. 25, 2009]