Zend Config tree solution
The best part of my favorite PHP framework, Zend framework is Zend_Config. With Zend Config you can run you web application with more power full configuration that any one can change your application setting for use.
Read more information about Zend Config at Zend framework manual for Zend Config.
But in most web application you may have many configuration file with special format such as INI, XML or PHP . Also some of configuration is for one part of your application and may you put in special folders.