If you have any modules that add external JavaScript to your pages (like Google Analytics), make sure you have the line

<?php print $closure; ?>
in your .tpl.php files right before the end tag. If you don't have this line the external scripts will not be loaded and will not be added to your pages.

This should be the first thing you should check if Google Analytics is configured correctly on your site, but is not showing any data in the Google Analytics reports.

php print $closure