BuddyPress.org

function here_are_my_stats() {

?>

// Put your statcounter/google analytics/whatever javascript code here

<?php

}

add_action( 'wp_footer', 'here_are_my_stats', 999 );

Put it in a PHP file and drop into mu-plugins.

If you use Google Analytics, you can filter by subdomains: http://www.google.com/support/googleanalytics/bin/answer.py?hl=en&answer=55524

Yup, that code will add an arbitrary piece of code into the footer, just before the </body> tag.