When I first started working on e-commerce sites, choices for Drupal-native carts were limited to two packages: the e-Commerce project and Ubercart. Based on the development activity and large number of supporting modules, I became an enthusiastic supporter of Ubercart. In fact, it's was my first choice for ecommerce systems in general, since it brought so much to the table: Here's a scalable e-commerce solution using Drupal's same node-based architecture, theming system, and user management routines while offering a cart with a barrel full of sophisticated customization options. If you needed both a CMS and an ecommerce solution, you'd be hard-pressed to find a better combination than Drupal 6 and Ubercart.
Over the years, though, I've tempered my enthusiasm for Ubercart: While it's still good at handling the most common ecommerce demands, the project is not without its flaws. Its documentation can be thin, responses from the community sometimes slow, and chunks of more advanced features are sometimes left frustratingly unaddressed. None of this is helped by the project's home site which can be difficult to navigate if you're looking for quick answers to common questions.
But Ubercart is still the best game in town for Drupal 6, and it continues marching on — Ubercart 3 is a port of the project to Drupal 7, and there is a committed developer base currently at work. Lately though, the choices for Drupal 7-native shopping carts has gotten bigger, with the introduction of Drupal Commerce.
Commerce is an exciting entry to the Drupal shopping cart category written by some of the same developers who previously managed Ubercart. (It's lead developer, Ryan Szrama, was the former Ubercart lead.) Unlike Ubercart, Commerce is a Drupal-7 only module. While it's technically been in development since 2009, it wasn't entirely ready for production and it's only been wIthin the last few months that package downloads have gained momentum. Meanwhile additional support modules are rounding out the project's offerings, making it a serious option for new installations. So how do the two compare?