I get a sound that's sort of half-click/half-rattle whenever the clutch is engaged (pedal released). It started soon after I had the clutch replaced, and like your sound, goes away when I depress the clutch pedal. In my case, I think it's just the t.o. bearing rattling against the throwout flanges on the pressure plate assembly. It hasn't caused any drivability or reliability issues (if it was gonna break, it prolly would've by now), and is easily abated by increasing the radio volume.
Is there any way you could record a sound clip of your clicking noise and post the sound file somewhere? Maybe take one recording near the bell housing, one near the body of the tranny, and one near the transfer case?