Comment How To Diagnose a Suddenly Slow Windows Computer (Score 2, Interesting) 835
I think you'll find these two presentation videos helpful:
1. The Case of the Unexplained -- http://www.microsoft.com/emea/spotlight/sessionh.aspx?videoid=722
2. Advanced Windows Troubleshooting with SysInternals Process Monitor -- http://www.microsoft.com/emea/spotlight/sessionh.aspx?videoid=346