Stefan Reuter has a very quick example of a method for profiling your PHP applications with Xdebug and KCachegrind.

Ever wondered where your PHP applications spend their time? [...] We wanted to gain performance insights of a newly developed application based on Zend Framework to spot areas worth receiving some fine tuning. We did not want to modify the application for that purpose so I had a look at the options available for PHP.

The resulting combination of XDebug and KCachegrind to grab the stats from the application and create great output images/reports to help make locating the problem a snap.