You can 'include' all sorts of code in various sections of any given page. For example,
include('../includes/functions.php'); // This is at the top of every page, and contains the function: validate_session()
include('../includes/inetdb_connect.php'); // This is at the top of every dynamic page to connect to the database
include('../includes/lt_navbar.php'); // This is in the body of every page and displays my entire left navigation bar, complete with links
// etc...
The benefits are obvious. When I change a link in my navbars, I only have to do it once. If a particular function is broken, I only have to refer to one file to fix it. If I decide to change the password to my database, I only have to modify one file.
Just bear in mind that the code in your includes needs to use absolute web addresses (not relative addresses), since the pages that include them will most likely have different paths.
In other words,
<h3>Department Pages</h3><!-- Links to various departments -->
<ul>
<li><a href="http://www.domain.com/departments/it">Information Technology</a></li>
</ul>
NOT,
<h3>Department Pages</h3><!-- Links to various departments -->
<ul>
<li><a href="../departments/it">Information Technology</a></li>
</ul>