Old answer: Could be turn signal or hazard flasher.
Additional answer: I had a similar problem. The short answer is that a factory recall may fix it. See my long answer at the link below.
http://markdionne.blogspot.com/2006/11/2000-vw-gti-clicking-noise-behind.html
I may be slightly off, but I have noticed the 'click' for the flasher is coming from the hazzard flasher button. I have removed the harness and found the turn signals do not work as long as the switch is disconnected. Hope this helps!! Just replaced mine. The Emergency Flasher switch (button) on the dashboard serves as the turn signal flasher also. Around a $35.00 item. You have to disassemble the face of the dashboard.. relatively easy, about 45 minutes.
on your car the flasher is located behind the instrument cluster beside the hazzard lights button.
on top of the steering collom
the relay is located within the hazzard flasher switch. If faulty replace flasher switch and it will sort out the problem
The turn signal flasher is located in the same assembly as the hazard button the dashboard just above the stereo. You need to remove the trim pieces from the dashboard in order to access the flasher assembly.
No they are not. The hazard flasher should be located in the fuse panal. While the turn signal flasher is located behind the dash near the AC controls. Can be a pain to find and replace.
The flasher is located under the dashboard on the drivers side above the fuse panel. It also depends on what year, make and model you have.
The flasher relay switch is located beneath the dashboard, on the drivers side. The flasher handle is located on the left hand side of the steering column.
The 2002 Geo Tracker flasher relay switch is located beneath the dashboard, on the driver side of the passenger compartment. The flasher relay switch simply plugs in and out.
The flasher relay switch can be located beneath the drivers side dashboard. The flasher relay switch will be above the brake pedal.
The 2004 Toyota Tacoma flasher relay fuse is located beneath the drivers side dashboard. The flasher relay fuse is actually a relay switch.
Left of the steering column, under the dashboard.