Two things come to mind:
- Excessive (very excessive) spotlight indexing
- Drive or drive related problems
You can check spotlight using Activity Monitor. Setup Activity Monitor to list all active applications, not just yours, then sort them by name. If you see the process named mds and it's worker threads which will be named mdworker and the CPU percentage is high then it's spotlight. This was a problem on older (Tiger, Leopard) systems but they've gotten it pretty well cleaned up on Snow Leopard and Lion, unless there's some type of problem with the spotlight files that are causing it to cycle.
Personally, I would guess it's the hard drive. Disk Utility will not tell you anything about drive problems unless they're terribly obvious. On basic checks all it does is verify the integrity of the system.
What I would do is go to SCSC's web site and download the free demo of Scannerz. It now includes their book Hard Drive Troubleshooting which is for Mac's and it's all free. The demo program will only scan the first 10GB of the hard drive, but Scannerz is fault identification software, meaning surface scans aren't the only things it can analyze. The link to the site is:
http://www.scsc-online.com
I would do the following:
- Download the Scannerz Demo under their Scannerz section
- Stop all programs (everything!). It has to be the only thing running
- Run a scan in cursory mode, which will end at 10G (demo limitation)
If the scan comes back with any errors or irregularities, rescan it and see if they're repeatable. If they're repeatable you have bad sectors on your drive. If they're not, there's likely a fault somewhere in the system. Their book goes into detail on how to isolate the problems. If you have a surface scan error that's beyond the 10GB range, unfortunately you won't be able to see it. You might want to look at some of their videos of scans on failing drives which you can access from the Scannerz section too.
Good Luck.