I've done dozens of ecommerce projects and suggest the following. If you need a good turn key system that's full featured, easy to skin, and turn key, I'd consider Pinnacle Cart (php/mysql). If you need a good open source system, I'd look into Magentocommerce. Its much newer than oscommerce and has received excellent reviews. I am still working to figure out how to skin it, as it uses a different approach to skinning, but should be more flexible in the long run. (php/mysql). Another good one is Interspire. Again a much newer cart (not open source), but also using a lot of newer web programming techniques. (php/mysql).
Tom Christensen www.actiondigital.com