Sounds like your hard drive could be going bad.
The click could be the heads of the HDD resetting.
If you restart your PC, right after the system posts all the heads of the HDDs reset, listen and see if its the same click or not.
Or your PSU could be going bad and not even good power to the HDD making it act funky. Though if this was the case you would have other instability problems.
I have a Vantec external laptop HDD encloser which has 2 USB 2.0 ports in it. The 2nd USB port is to supply the encloser with more power incase it needs it to run more power hungry drive. (With out the need for an AC adapter)
If I only plug 1 USB port into the enclose the drive will click every few min and stop transferring data for a few seconds after that.
I plugged in the 2nd USB port to give it more power and the clicking stopped and transferred smoother after that.
If the HDD in question is the Seagate in your sig, go to the seagate site and download Seatools and see if your drive passes the testes.
EDIT: Not sure if this actually does happen but if I remember right some types of windows crashes let the HDD reset (which causes the click) and the drive might not be bad at all.