I've answered the exact same question here: IIS6 CPU Spiking
Below is the text from my answer:
How many App pools? You can start by moving your websites into separate app pools and then using task manager + command line iisapp to match up which app pool matches which task. That will help you identify which web it is to start with.
Once you have that identified grab the microsoft IIS debugging tool: http://www.microsoft.com/downloads/details.aspx?FamilyID=28bd5941-c458-46f1-b24d-f60151d875a3&DisplayLang=en
Using IIS Debug Diagnostics to troubleshoot Worker Process CPU usage in II6
Failed request tracing in IIS7 can help track down many performance issues with websites, but we still have a broad customer base on IIS6. Troubleshooting performance issues in IIS6 has been quite difficult until Microsoft released a set of tools that gave greater insight into analyzing a stack trace.
The IIS Debug Diagnostics Tool can help track down CPU and memory issues from a worker process. Microsoft has a nice kb article that goes over the basics as well: http://support.microsoft.com/kb/919791.
Install the IIS Debug Diagnostics locally on the system.
Open the Debug Diagnostics Tool under Start > Programs > IIS Diagnostics > Debug Diagnostics Tool > Debug Diagnostics Tool.
Click Tools > Options And Settings > Performance Log tab. Select the Enable Performance Counter Data Logging option. Click OK.
Use task manager to find the PID of the worker process.
Select the Processes tab and find the process in the list.
Right-click on the process and select Create Full Userdump. This will take a few minutes and a box will pop-up giving you the path to the dump file.
Select the Advanced Analysis tab and click the Add Data Files button. Browse to the dump file that was jump created and click OK.
Select Crash/Hang Analyzers from the Available Analysis Scripts box for CPU Performance and crash analysis. Click Start Analysis.
After a few minutes, a report should be generated containing stack trace information as well as information about any requests executing for longer than 90 seconds. Note that the memory dump with use a few hundred megabytes of space, so be sure to install the tool on a drive with sufficient debugging space. Also, if the box is under heavy load, you can create the user dump on the system, copy the file to your workstation, and perform the analysis locally.