I ran across a full shopping cart using CI called opencart. it seems promising and worth a look
OpenCart doesn’t use CI… but it is probably one of the best options out there right now.
I just edited my post from a while ago because I didn’t want to give bad advice. Magento is a beast and not a viable option.
Since that post I also tried virtuemart and I may dare say it is the same if not worse then oscommerce.
I also found opencart about 6 months ago and I really like it. I totally agree it is the best coded option but it really needs more features before it is a real option. It is perfect for small stores with less demanding needs at this point. The loader is almost identical to CI, the MVC folder structure is pretty close too as well as some other things. I asked the developer about it and he said he did use, I forget, CI or Kohana as inspiration for some of the code. Just wish it had the features of the big carts.