i\'ve seen alot of php based websites where no matter where you navigate your stuck at the index.php and some random parameters are passed in the url. and when i take a look
You are looking at websites built with a front controller.
http://en.wikipedia.org/wiki/Front_controller
Many popular PHP apps like Joomla use it to treat a collection of scripts as a cohesive application.
A front controller is a good idea for languages like PHP, but remember to hide the front controller with something like mod_rewrite to create URL canonization and to optimize readability.