After talking with Martin and Jordan about the best way to include Google Analytics code within Moodle installs in a theme independent method it was decided that the easiest way presently would be to introduce three new config settings that would be inspected and then echoed into the page at appropraite points.
This way the site admin could easily copy/paste such JS or HTML into the config settings and know that no matter what theme or page is being used it will be added.

Cheers
Sam