Sounds like you want to implement a Single Sign On framework. Basically when you first see the user, if you don't know them, you redirect them to the single sign on server. Wich authenticates them and redirects them back to you with a authentication token. You verify the authentication token with a web service call to the SSO server. Ff it is valid then you mark that user as signed on.
EDIT
So thinking about it more and reading tovare's answer and your comments. Why not create some javascript code that works like an google ads? You put the javascript on the page and it does an a request to your central tracking server using a dynamic iframe.
Have your tracking server return an image tag with src of the unique id (its own session id) embedded.
<img src=contentserver.com/track.php?id=12345668>
The content server has a server side script (track.php above) that maps its local session id to the unique id received from the tracking server.
The unique id stays the same across all sites.
Edit2
Instead of using an image, use the javascript trick. The content server just requests a javascript file from the tracking server. but the file is a dynamic one generated on the server side. it returns a generated javascript function called unique_id()
it returns the unique id from the tracking server. Call the track.php using ajax to determine if this is a unique user.