andrea, yes WP e-Commerce (http://www.instinct.co.nz/e-commerce/) works almost well on WPMU.
There are several small issues I'm having with WPMU 2.6.5 and e-Commerce 3.6.8
1. Default settings aren't properly 'generated' when you activate this plugin for a newly created blog.
Workaround: you should create a new post/page and add some content like image, video, etc to it. After that when you activate a plugin those default settings are OK. Very strange behavior :)
2. The plugin does not automatically create it's directories inside blogs.dir/<blog_id>/files/..
It needs 4 or so folders created there, but the plugin fails to create them. It'll give you a warning. After you create those folders manually - it's all OK.
3. I remember issues when using WP e-Commerce and auto-activation feature of plugin commander, although I think most recent versions of both plugins are free from that error - at least I don't get it anymore.
4. I could not get WP e-Commerce working from mu-plugins folder.
Seems, that's it :)