Something's eating my CPU... ?

Something is using up a large chunk of my CPU. I can see that the CPU is running at 10-20% but performance is affected in a jittery way when playing games and other things. I can hear it busily doing something in the box, which makes me think the HDD is busy. However, in the processes tab of task manager only task manager is using any CPU (equally either 0 or 1 cycles). I've killed off things like sidebar trying to isolate the issue. As far as I can tell, windows is simply refusing to tell me which services it's running to chew up my cpu (intel quad 6600).

This doesn't happen all the time, and for a while now Vista's indexing tool has been the main culprit. It's been set to only index a bunch of document formats, emails, pictures, things I basically recognise.

So a couple of questions:

1. Does anyone know what is causing the problem on that information?

2. Is there a way of revealing hidden processes chewing up CPU so I can better identify the problem?

3. Is it possible to isolate all of windows' functions and frustrations to a single core and otherwise leave me in peace to run games or other programs without the irritation of some essential task.

(PS. Antivirus is nod32 and it's not scanning.)