I have used both plugins. I tested them both extensively and have built and delivered client websites on both platforms. My tests were conducted over a year ago before I went with my preferred (Shopp) but here is what I found.
WP Commerce at the time had buggy code, poorly written markup and many elements were not given classes/id’s making it hard to format via CSS. Support was almost non existent in fact I got better support from a guy named Shayne Sanderson who isn’t even one of the developers (wrote an unoffical guide to the plugin though).
Their forum was poorly tended and the plugin was poorly documented.
Matt Mullenweg mentioned at a recent WordCamp that they have rewritten the plugin to use Custom post types. So they may have improved their code since I last looked.
Shopp on the other hand has proven to be more robust, better coded, and much better supported (at the time of testing). Yes they are a paid for plugin but they are also totally GPL. Their forums are well tended and questions are usually answered by a developer and with minimal delays.
WP commerce does have paid modules for their plugin which can extend its functionality beyond that of what Shopp can do but Shopp is far better documented for those interested in extending it’s functionality themselves.
At the time of testing both provided the same core functionality and both handled the same payment options. I personally preferred Shopp as it was easier to get up and running, integrated with themes with less tweaking required, and was easier to use (for the client). The superior support was an added plus.