Here is a good article to help you.
I recently wrote a blog entry: Monitoring Windows Server CPU performance. In other postings I discuss a lot of application performance considerations. I would also suggest also looking into the Performance Analysis of Logs (PAL) tool. The PAL tool is described by the website as below:
Ever have a performance problem, but don’t know what performance counters to collect or how to analyze them? The PAL (Performance Analysis of Logs) tool is a new and powerful tool that reads in a performance monitor counter log (any known format) and analyzes it using complex, but known thresholds (provided). The tool generates an HTML based report which graphically charts important performance counters and throws alerts when thresholds are exceeded. The thresholds are originally based on thresholds defined by the Microsoft product teams and members of Microsoft support, but continue to be expanded by this ongoing project. This tool is not a replacement of traditional performance analysis, but it automates the analysis of performance counter logs enough to save you time.
I have used this tool several times to show that the network is not the problem. The counters in the templates that come with PAL also have pre-set threshold values. You can edit the values and set your own thresholds. This should help you get started. Feel free to come back for more information and let us know how you get along.
In the IT trenches? So am I – read my IT-Trenches blog.