Are you running Standard Edition or Enterprise Edition of Windows Server 2003? If you're using Enterprise Edition, you could install Windows System Resource Management (WSRM) and restrict the CPU used by W3WP.EXE.
But, that aside, I'd first want to understand why W3WP.EXE is consuming so much CPU. Your tools here are both from Microsoft SysInternals: Process Explorer and Process Monitor.
Use Process Explorer to confirm that it is W3WP.EXE causing the issue, and get a more in-depth understanding of its CPU, I/O and memory usage. One thing to be sure of here is your available memory and paging activity. Do you need more than 4GB, for example. I don't know how much your STORE.EXE is using. However, don't go beyond 8GB for an Exchange 2003 server.
After this, use Process Monitor to actually watch what its doing. Configure a filter for "Process Name IS W3WP.EXE", and select "Drop Filtered Events". Now, you'll be watching just your worker process.
If nothing shows up, clear the default filter that excludes activity from the "System" process. The reason being, I think this is where you'll see your HTTP activity.
This might give you some clues as to what's going on.
