I want to monitor I/O of a Windows 2003 server system. I'm specifically interested in the I/O activities of specific directories (where I have an unknown and ever changing number of files). I have a rough idea how to monitor a complete disk or partition, but not for "just" some directories. How would I do that?
Try the SysInternals tool Process Monitor. It monitors quite a few different types of activity on your system (registry access, file access, network activity, etc.).
It has pretty flexible filtering. For your case you could do something like this: