In my world view there are only two viable well coded options:
An affordable paid cart that has so many features and the code is as elegant as codeignitor:
Interspire Shopping Cart
Interspire has simple code and a ton of features not to mention that they really put your money to good use and add a ton more features every 6 months like clock work and add bug fixes every week or so. You even get free upgrades and support for a year. Then after that there is a friendly forum community.
UPDATED:
I no longer recommend Magento…the code is very cryptic and convoluted and I think it may be intentionally done by Varian. You will notice that their documentation does very little to help with development while a lot for themeing and administering the site. Also it is a SLOW application and would have a difficult time running on a shared server with heavy load and many other websites. The main goal of Varian is to make boat loads on the cart and you can see their support, pro cart pricing and code shows that intention. I’m not saying it’s not possible to modify it but plan on spending two to three times the development time doing it and having to charge your clients to do so. With practice you may get quick but not quicker then with other carts that are well coded.
I don’t have any update for a recommended open source cart because I have only used and coded with oscommerce and its branches, virtuemart, magento and opencart. Out of all those the only one well coded was opencart. It is MVC based and to boot the loader class and other code is just like CI BUT it is seriously lacking in features and thats the only reason I can’t recommend it yet.
—-SEE UPDATE—
Then Magento which the code is a bit cryptic and slightly boxed in but the quality of the code is light years ahead of oscommerce and any of it’s derivatives. Once you build an extension or two and if you understand overloading of classes and configuration based frameworks it will click and you will love it.
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Now I highly recommend and almost insist that anyone building an eccomerce site stay away from oscommerce or it’s branches like zen cart and many others. They are insecure and they break when server technology is updated. They are completely buggy and a lot of the modules are created by inexperienced programmers. I know a couple of oscommerce sites myself that have been hacked or show errors all over the place.
There’s my rant…thanks for listening!