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They set up a big template on thier site, usually just a plain layout, then they have something like <?PHP include("$page.html"); ?> where they want to include content. its very useful for sites that change thier layouts a lot.
The best newbie tutorial that I have seen is Here.
So when you see a 'page.php?var=stuff', that means the URL actually includes a variable that you can access via PHP. I was looking at that tutorial the guy suggested and I didn't find anything about this, so I hope this helps.
Yeah, you can still do whatever you want to do with variables inside of other includes. On my site, my single front page must consist of 20 or so various includes on various levels. The server won't send the webpage to the browser until all parsing is done... and that's includes all includes().