I recently found a tool that can help do performance analysis on servers in your environment. This tool gathers the data from the Performance Monitor and does some level of analysis to help diagnose issues. It is especially good at IIS 6.0 and Active Directory.
From the Overview:
Service Performance Advisor is a server performance diagnostic tool developed to diagnose root causes of performance problems in a Microsoft® Windows Server™ 2003 operating system, particularly performance problems for Internet Information Services (IIS) 6.0 and the Active Directory® directory service. Server Performance Advisor measures the performance and use of resources by your computer to report on the parts that are stressed under workload.