I have this really weird ticking noise in windows XP, I dual boot windows vista X64 and in windows vista I do not have the ticking noise. The noise comes from my speakers and not my computer. I am sure of this because when I turn off my speakers the ticking sound stops. The ticking noise occurs randomly and it is really annoying, it's not a hard sounding noise but it's just hard enough to get you annoyed.
I had the same problem on my HP Pavilion laptop. It turned out to be the DigitalPersona fingerprint reader. Right click the icon in the tray, select properties and uncheck 'Enable sound feedback'. I think it's a bug but it worked for me.