Hey, I've been having this problem for months now and countless mechanics have been unable to help!
I have a late 03 Passat Estate S TDI with a real heavy clunking under the bonnet, I've had suspension arms, track rods and both main hydrolic engine mounts replaces (upon advice from VW inspection) but the problem is still there!!
It is definitely a heavy metal on metal clunking which happens on bumbers roads and really badly on the motorway when lifting off at 80mph made worse when under light braking!

Could this possibly be the front engine (snub) mount???

This is the only other thing i can think of, is this a major job to replace?