Check out
viewtopic.php?f=5&t=62293&p=689656&hilit=mount+motor#p689656 . I'm assuming you have eliminated a transmission issue such as low fluid. If so does it do this when you shift between park and reverse with your foot firmly on the brake? If so I'd wonder a bit about a clunk associated with taking up slack in the drive train possibly a CV joint, a drive shaft u joint, or the slip joint at the back end of the drive shaft or I certainly hope not in the differential but I doubt the latter. Have someone outside the car listen for the sound at ground level (NOT with head under the vehicle) and see if you can locate the area of the sound. That said my personal bet is one or more motor mount has failed. The common failure mode is internal and not something that is visible on the vehicle unless the mount physically collapses such that the lowest portion of the engine assembly almost touches the cross member; there has been one post of this happening. Most of the time they fail internally such that when removed from the vehicle and shaken they rattle internally. Failed mounts cause all sorts of weird sounds both when the gears are shifted and during operation and those sounds tend to travel in weird ways thru the vehicle body.
If it was mine I'd be inclined to pull the passenger side mount, per the GDE instructions at
http://www.greendieselengineering.com/f ... t/115.page, and give it a good shake. Removal of the passenger side mount is relatively easy, driver's side less so. If it's bad replace and it would be a good idea to replace the driver's side mount at the same time if the passenger mount is bad. NOTE both mounts are identical except for the removable heat sheld so if you need 2 buy the 2 cheaper ones and move the heat shield.