I had exactly the same problem with my 300tdi. There are two causes.
Firstly the lift pump can cause this noise if the small rod breaks and is then still being driven up and down...
So you can check your lift pump operation, this can be done by loosening the lift pump out pipe, and then pumping the lever a few times, diesel should spill out. If not turn the engine over on the starter one/two blips to get the cam shaft to sit at the opposite position. Try the lever again, if no fuel spills out then your lift pump is gubbed, unbolt the old one, new one on job can be done for about £30. I had to renew the fuel lines from the pump to the filter, and take a piece of hose over the original incoming pipe and jubilee clip it onto the new pump as the fittings were different. Also note you will need to take the injector pipes off, as access is impossible without these removed.
Also, I know you could say that if the lift pump was broken then the engine would not run properly, this is not true, as I had a broken lift pump on the 300tdi for about 3000miles and the only loss in performance was accelerating hard while at speed.
Now, if the above test went sucessfully and its not the lift pump then its the injection pump, I got rid of the clicking noise by running some fuel cleaner stuff through the engine, cleaned the gunk out a bit...
I had both these issues, I also had it for a long time before I looked for it... so I would not worry to much about it.