I'm using WinXP, and I notice that in the Task Manager, on the Performance tab my CPU usage is 100%. But When I go to the Processes tab, and sort by CPU System Idle Process is taking up 90%. I've double checked that things like AVG anti-virus isn't actively scanning, and that jkdefrag is not defragging. But I know something is taking CPU cycles, because the machine is very slow. How do I determine which process is hammering the CPU if it doesn't show in the Process List?
Process Explorer is a much better tool for inspecting processes than the built-in Task Manager. While it might not answer your question completely, it may give you more insight into the problem.
Make sure that the "Show processes from all users" checkbox is checked at the bottom of the process list in Task Manager, so that all processes are show.
I was having a similar problem a couple of days ago and it turned out the machine was infected with a Rootkit. Since removal things seemed to have calmed down.