On PHPMaster.com today Matt Turland has an article posted about using XHProf and XHGui to find the performance issues in your application and profile them to help optimize things.
Profiling is the process of measuring the execution time of each function or method call involved in servicing a single page request. The data collected from this process can reveal issues such as a particular method taking a long time to execute or being called a large number of times. Profiling a PHP script generally requires installing a PHP extension. The two more popular extensions for this purpose are Derick Rethans' Xdebug and Facebook's XHProf. This article will focus on XHProf.
He walks you through the installation of both and shows you some sample results of the profiling of a simple application and how you can compare the results across profiling runs. Additionally, if you install graphviz support, you can generate the call stack output in a visual form to make for easier consumption.