Bruce, I've done it many times. There is no one single solution. At the moment I have two sites that actively sell online and both use completely different systems to do so. It all depends on the business model ur trying to implement (straight retail and shipping, drop shipping, digital content, large quantity of different products, etc.)
Send me an email directly and I'll do what I can to offer some suggestions on the best system to use based in what your trying to do.