I am not sure there is such thing as the best shopping cart software, however there are many shopping carts out there depending on what you want to sell with your online store. The two open source shopping cart mentioned about are fine, there are also bespoke shopping cart such as the shopping cart website offered by Velnet and the one in my signature will will help you sell online.
You can also look at carts such as the one offered by rent a shopping cart.

By these 2 already mentioned, I would maybe add osCommerce.

I'm not to bothered about which is the best shopping cart, we use shopfactory for our own shops, the thing I would like advice on is how can we sell low priced items without Pay-Pal and all others taking the cream off our sales? if anyone out there can help me I will be over the moon.
David

I think the same, Magento is the best... Zencart and VirtueMart right after it...

Boss Cart could be a good choice...

AJ Shopping cart is the best php based shopping cart software.

I also consider Magento to be the best ecommerce shopping cart available.
There are so many useful functions in it.

OSCommerce, Zen Cart, Magento ....

Search More Here: Open Source eCommerce Scripts - OpenSourceCMS

I can see that a lot of the shopping cart software mentioned is free, I would not advise using free shopping cart software, my main reason for this is that every hacker in the world will have downloaded and analysed it and found every back door into the sites making it insecure and tbh I would not want to be putting my bank detail in and buying online!!!

I would for absolute shopping cart and our software costs £19.99 per month however it is completely secure and includes alot of good features, but most importantly it is very search engine friendly and we have alot of good rankings!

If any one is interested or has never heard of it go have a look, I cannot add links at the moment but if you go to google type shopping cart we are number 4, absolute shopping cart.

I would be very interested to hear your thoughts!