Running scripts from a subdir

Another one of those questions where I think I may be missing the blindingly obvious.

If one has a script subdir in the root directory, i.e: [forum-root]/subir/script.php, one can set PUN_ROOT in the scripts to point back to the root dir, but is there a global way of making header.php and such look in the root dir for the various links/paths to scripts, rather than the pwd? For example, out of header.php:

<li id="navuserlist"><a href="userlist.php">User list</a></li>

which means the link will be referenced to the pwd instead of the root dir.

Cheers,

Matt