I just stumbled upon a fresh post by Hal Rosenberg, a Performance Engineer from VMware. Its a great doc, titled Performance Troubleshooting for VMware vSphere 4. It has some great flowcharts and steps to take to come to a root cause analysis for performance issues. Although it is written for vSphere 4, much of the methodology applies to earlier versions as well.
Another great job by the VMware Performance Team! Thanks Guys!