Check out this open source php webstats script for when you want to track multiple domains.

It features a logging engine that, either invoked as a web-bug by a HTML <img> tag or embedded with two lines of code into your PHP application, logs each request to a website into a database. One installation of phpOpenTracker can track an arbitrary number of web-sites.

Through the phpOpenTracker API module you can easily access the gathered data and perform complex operations on it, like for instance the analysis of your visitors’ clickpaths.

The analysis of clickpaths is essential when you want to measure the usability of your website. phpOpenTracker’s API functions ’shortest_paths’ and ‘top_paths’ help to answer questions like: Is the navigation intuitive enough? Do visitors find the shortest, most direct way from A to B? How are ads perceived? On what document do they leave the website — and where to? The answers to these questions help you to improve the user experience and the way your website is percepted by your customers.

Edit: another nice php stats package that works on multiple domains from one back end is http://www.phpmyvisites.us