I gave WP-Piwik a 5 star rating. it works very nice on my multisite install (WP 3.2.1 with Multi-DB). But I'd like to add some thoughts here after I had a hard time to figure out some strange occurrences. Maybe this helps someone...
I had installed WP-Piwik some while ago on my multisite and at that time worked just fine, adding new sites to Piwik. Some site upgrades and tweaking however left me suddenly with site stats that did not really belong to freshly created sites and the sites didn't get added to Piwik. First I suspected the newly introduced Multi-DB, but since there are no WP-Piwik tables required, Multi-DB was not causing this. there were basically two things that got mixed up:
1. It seems upgrading the plugin overwrites the multisite config setting though and it might be a good idea to have them in a separate config file, that does not get overwritten upon upgrade. Had to set it back to multisite=true.
2. Also experienced a strange behavior in connection with wpmudev's new blog templage plugin. Making a previous site (with activated piwik stats) into a template for new blogs will replicate the template site's stats on the newly created site and the new site won't get added to Piwik. It took me some time to figure it out, but in order to prevent this behavior, one needs to clear out the db field wp-piwik-settings from the wp_(siteid)_options table of the template site. Once this field is empty, the newly created site will generate its own footer script with its own ID and the site gets added to Piwik.
Just thought I leave a note about this here, as I could not find it documented anywhere. Maybe this will help someone else.
Thanks for the great plugin Braekling!