I was playing with my Sony portable, formatted the hard drive, and it started clicking each time the drive spins down. It is a PCG-GRX500P.
The solution is to go support.intel.com download the Application Accelerator (version 2.2.2 because they removed mobile chipset support from the most recent version) find the disk drive, and change the drive power management setting to “Maximum Performance”.
The clicking was parking the drive (I think) every time activity dropped for for a few seconds.