I'm guessing you are moving from Windows 2000 to Windows 2003. On IIS6 Web sites (and applications defined within them) now use a dedicated concept of an Application Pool defined within IIS manager rather than use the original COM+ applications.
However in both cases there is an option to shutdown the process if it has been idle (that is no requests have been processed) for a period of time.
The upside is that the memory and other resources being occupied by the process is released.
The downside is the cost of spinning the process back up again and the restoring of any application level data whilst a user request is waiting.
For intranet applications or where the server is dedicated to serving a small set of specific sites enabling idle timeout is probably not a good idea.
Where you have dozens or hundreds of websites you probably host groups of these in the same application pool on IIS6 so again enabling idle timeout is probably ineffectual.
The only time I could see this being useful is a website that performs some heavy operations, is rarely used and installed on a server that has other duties.