I have my Drupal installation in a subfolder on the server, so all my links are of the form: http://example.com/drupal/admin/etc.
In Drupal, you'd normally change the $base_url variable in the settings.php file to reflect this and hide the subfolder from the URL, but because I'm also using Domain Access, I can't change it.
I therefore went looking for a way of hiding the subfolder from the URL, and finally came across this post: http://drupal.org/node/217710#comment-718517
By adding the provided code to my settings.php file, I was able to hide the subfolder from the URL, and without breaking Domain Access!
I'd like to recommend that the code be added somewhere (install.txt?) so people in similar situations don't spend hours pulling their hair out like I did ;)
* Set dynamic $base_url to remove subfolder from URL
* See: http://drupal.org/node/217710#comment-718517
$base_root = (isset($_SERVER['HTTPS']) && $_SERVER['HTTPS'] == 'on') ? 'https' : 'http';
$base_url = $base_root .'://'. preg_replace('/[^a-z0-9-:._]/i', '', $_SERVER['HTTP_HOST']);