You symptoms are consistent with seek errors on the hard drive - the OS pauses waiting for the hard drive to thrash itself to pieces trying to move the drive heads to the next chunk of data.
You can run "verify disk" using Disk Utility - if it finds any errors, this may provide an additional indication of impending hard drive failure, and YOU SHOULD BACK UP THE DATA ON THIS DRIVE AS SOON AS POSSIBLE!
If you have an iPhone or iPod Touch, download DriveSaver's excellent free hard drive simulator app:
http://www.drivesaversdatarecovery.com/ep/drivesaver_app/
and compare the noises coming from your machine.