I think a perfect Piwik integration into ISP Config3 would be just to add a radio button "Piwik" next to Webalizer and Awstats.
When enabled, this would (via a web service/Piwik API) create a piwik user for the website and return the user ID.
Then two radio buttons would display :
- manual integration (default) : display the JS code with user ID (like in Google Analytics).
EDIT : Or maybe there is a way to insert a JS tracking code without a siteid (then Piwik would "detect" site from its referer domain ?). I haven't found such an option on Piwik site though... I'm thinking about this because we'll soon have to migrate hundred of sites from Awstats to Piwik and that would be nice if we could juste create all sites in piwik and then enable apache filter for all websites.
EDIT2 : In our setup, Piwik will be installed on a separate VM because it will handle all our websites stats, that's why I suggested an integration with ISP COnfig using web services and/or Piwik API.