I don't have much time to browse the MT forums – but had some "downtime" this afternoon to do so. There's often a lot of tricks for PHP in there. I found this thread, and towards the bottom, phideaux posted a neat trick to make using includes in your code easier.
The idea is you always use one directory for your includes. In your .htaccess file you add this line
php_value include_path ".:/home/user/public_html/includes"
Then any time you want to use an include in your file, you don't have to deal with typing out the big long absolute path (ie. /home/user/public_html/includes etc etc). All you need do is this:
<?php include("header.php"); ?>
Neat trick!