Hi Jenn
Great question, and I'm sure many entrepreneurs who are new to ecommerce are asking the exact question while trying to choose the right shopping cart.
Let me share my thoughts about free shopping carts.
If you have an absolute zero budget, and just want to test and learn, free shopping carts might be the best resource to start learning. There are even many successful ecommerce companies who have been still running a free shopping cart. But most of these are using a heavily customized versions of these free carts.
You should place free shopping carts into two categories.
Free Open Source Shopping Carts: One of the most popular open source free shopping carts is osCommerce. As a mainframe, it is a pretty good one. The best advantage is; it is free :)
But what are the disadvantages of open source carts similar to osCommerce?
Since they are open source and free, they are preferred by thousands of ecommerce businesses, and they get hacked a lot. They are more vulnerable than paid shopping carts, higher usage numbers being the main reason.
You need to be updating all new patches constantly to keep your ecommerce site safe. If you have done some modifications to the main code, updating your free cart constantly will be much more difficult in the long run.
If you like to use a free open source shopping cart, you need to be very comfortable playing with the programming language (php, asp, .net, etc.) of the specific shopping cart.
Free Hosted Shopping Carts: Using a free, hosted shopping cart is another option. The huge advantage is agin it's free and you don't have to worry about instant updates. They are usually taken care of at the server side.
But what are the disadvantages of Free Hosted Shopping Carts?
They are usually very limited in functionality. Many companies who offer free hosted shopping carts end up with offering upgrade paid options after they have a good number of users.
Your shopping cart should be flexible and easily customizable depending on your company's needs. You won't be able to find the flexibility in free hosted shopping carts unless you run a very basic ecommerce store with a few products.
I hope this very brief introduction to free shopping carts will help.
Personally, I wouldn't start with a free shopping cart. Choose an affordable solution which fits your budget, and make your future expansion plan and consider your enterprise shopping cart options during the initial business plan.
Good Luck
James