I use Quickbooks 2006 for all of my accounting and currently have a EBay business but am putting up my own web site.
I have looked at various shopping cart programs such as VirtueMart, ZenCart, oscommerce, and CubeCart. I don't mind using one that is a pay one unless it's very expensive (such as Miva) but it seems many that are popular are actually free. It just seems that none of them work with Quickbooks and I prefer one that does. Of course I want a good all around e-commerce solution. I am using Joomla so that is why I looked heavily at Virtuemart but would consider others as well.