My questions is:

When including something on all pages, a top nav for instance.. (<?php include('topnav.html'); ?>)
What is the best way to have a page particular style like say you wanted the "HOME" link to stay underlined when you're on the home page.

The answer is most likely using javascript and I'm proabably posting in the wrong forum.

If necessary, you can move this to the javascript forum.

Would the best way be to give the body an id?

Thanks

Give all your links IDs, then insert a style rule for the "active" page into the document head using PHP

The way I sometimes do it, is I have a unique variable identifying the page. Sometimes, if I have pages with certain themes that are the same, I will also have a theme variable identifying which theme it is. I then use these variables as hooks in the PHP, and also as classes (I put $page as a class on the body, and $theme in the various includes, wherever is appropriate).