It's relatively easy to modify PHPAdsNew to cope with a whole network of sites, as long as you design the database that you write everything to is well thought out then you can do the reporting in any number of different ways. The scripting is relatively easy (I just use PHP and MySql), it's the design of your database and which variables you want to track that is tricky.
I basically only do organic SE traffic and PPC though so it makes things a little easier, if you had a trillion different types of traffic coming into your system and bouncing around things would be a little trickier. But I am a great believer in scientific advertising, John Caples is my idol.
