What you are hearing is thermal recalibration. (TCAL)
As a drive's temprature changes the platters expand and contract. To continue to read data reliably the drive must re-calibrate itself.
On drives that use aluminum platters, a TCAL every 20 to 40 minutes is not uncommon. If the drive is in heavy use (and therefore experiencing alot of temp changes) it may happen every 15 minutes. Drives that use glass platters (such as IBM's hardrives) will not have to TCAL nearly as often, maybe every 40 minutes to an hour (depending on usage once again) as glass does not expand/contract nearly as much as aluminum does....
Some drives will TCAL whenever it is needed, even right in the middle of a data transfer, thus making the data transfer temporarly stop until TCAL finishes. There are drives that will wait until they are idle to perform TCAL, these are known as "A/V rated" hardrives since they will not interrupt a data transfer to do a TCAL.
Personally, under my normal usage patterns my WD 800JB does a TCAL about every half hour. It does sound very similar to the clicking sounds the drive makes during power up. The sound is very quiet, and unless I am specifically listening for it I never notice it. (my fans drown out all noise from my HDs!)