PrestaShop

PrestaShop is a comprehensive, professional-grade shopping cart that is easy to use and setup.  The software offers a fully featured back-end interface to maintain your inventory, orders, shipping options and customers in real-time.  It is also highly customizable as you can incorporate your own modules.  PrestaShop keeps security in mind but securely transmitting customer payments directly to your bank account.

Magneto

Magneto is a robust e-commerce solution that offers unparalleled flexibility and control.  This software is so well designed and functional that you would never think it came from an open-source project.  Unlike other shopping carts, this one gives you clean URLs and SEO-friendliness right out the box, bypassing the need to make additional configurations.  Magneto has a scalable architecture and seamless integrate with various third-party applications.  Additionally, it gives you the benefit of both community and professional technical support.

CubeCart

CubeCart is one of the most popular shopping carts around.  Although it is free to download and use, you are forced to leave the developer’s copyright notice in your footer.  That disadvantage aside, CubeCart offers a plethora of features with support for most of the major gateways and shipping options.  The software comes with decent support from an active community that regularly contribute plugins to the cart.

Agora

Written in the Perl programming language and driven by a MySQL database, Agora is another popular choice for open-source shopping carts.  Very customizable, it features a built-in CSS (Cascading Style Sheets) manager that lets you control the look of the shopping cart as well as setup options ranging from a simple template-based storefront to more complex visual designs.  Agora supports unlimited products, a wealth of shipping and payment options, up to four tax zones at once and much more.

Zen Cart

Zen Cart is a user-friendly shopping cart that caters to beginners.  This is one software that actually focuses on the shoppers and store owners opposed to developers.  Zen Cart is easy to use and supports multiple shipping and payment options.  It also allows you to easily provide discounts and coupons to your customers.

osCommerce

The wide variety of features in osCommerce enables you to set up an online store fairly quickly.  It supports multiple currencies and also lets your customers print their invoices directly from the order screen.  osCommerce gets the backing of a superb community who provide ongoing support and make contributions to the project.

These are just some of your choices for open-source shopping carts.  Rest assured, there are many more to choose from.  While you can probably pay for something better, numerous users are doing just fine running their store with these free versions.