Personally, my favorite is X-Cart Gold. Paid product in the $200 price range. I've been using Magento a lot recently and like it and also InterSpire (new cart on the market but expensive - $1500+). It has all the featues you'd ever need.
Having used X-Cart since 1999 myself, I know it inside and out, and since it's a open source, I've had programmers modify the system to do extra things that I needed (like integrate an API to Comodo's SSL for automatic purchase and delivery of SSL Certs. We no longer use that system here as we had programmers write API for WHMCS, but for 2 years we used the X-Cart Module and it was perfect.
There are many good shopping carts, all of which have been named already. Depending on what you are adding to your site you could use something as simple as Paypal's cart, Google Checkout, or even Zencart. The best cart for your site won't be the same as the best cart for someone else. Figure out your requirements, then decide which is best for you.
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