I've got some experience with VirtueMart for Joomla, and I've found affiliate plugins for it as well. It seems like a good option.
However, like many people on this forum, I'm just in love with WordPress. Does anyone have any experience with any of the ecommerce plugins for WordPress? And how about integrating an affiliate plugin with it? I've not come up with much by searching Google, but I'm hoping someone has some experience with some plugins that can point me in the right direction. If there's nothing, I'll go with Joomla/VirtueMart.