On the NetTuts.com site today there's a new tutorial showing how to use XHProf to profile CodeIgniter-based applications and fidn the spots that are causing the most overhead/issues.
XHProf will provide you with a hierarchical profile of the functions your application calls, allowing you to follow the chain of events that lead up to resource intensive code running. You’ll be able to see exactly how much wall time (the actual time elapsed), CPU time and memory your application uses. This tutorial will help you get XHProf installed on your server, and integrated with your CodeIgniter application via hooks so that you can start profiling your application, in a production environment, straight away. Everything you see here was written for Ubuntu 10.04 – the latest LTS release at the time of writing.
They walk you through the installation of the tool (via a wget of the source), show you how to integrate it with CodeIgniter via hooks and include a simple class that is called to execute and report on the findings. Some sample output is included as well as some general tips on interpreting the results.