I've wrestled with this issue more than once, and what I finally had to decide is where my time and energy is best spent -- fixing code in broken shopping carts or developing new marketing campaigns. If you're a small shop operation just starting out, this is a no brainer. Find a one-stop solution for ecommerce (like Yahoo or GoDaddy), get something up and running, and use your time and talent to create revenue.

Believe me, I understand the drawbacks of going with the big site packages, but the fact is that their basic storefronts work...right out of the box. I've been managing several Yahoo stores for the last eight years, and while they have their limitations (okay, lots of limitations), that doesn't seem to stop the money from rolling in. Best part is that I can sleep at night knowing that all the back end stuff like the shopping cart, payment gateway, CC security, is someone else's problem, not mine.