If it happens sitting at idle with the clutch out and car out of gear check your clutches slave cylinder and throwout bearing. I would suspect the throwout bearing but must first ensure nothings wrong with the slave. This assumes you have no leaks in the master cylinder. I've never heard a differential click sitting still engine vibration or not. My experience with hondas is limited but I've had that clicking problem before with nissans and toyotas and when throwout bearings go they start making noise because the ball bearings get worn.