I had the same problem for a year but mine also happened on acceleration. You could hear it and feel it on the floor. I swore it was coming from the front pass side. The dealer test drove it and said they couldn't hear anything unusual but noted that there was a lot of play in the CVs. I and a friend replaced them and as soon as I pulled out of the shop... CLUNK! At LJS 2009, some nut job agreed to ride with his head under my KJ to better locate the origin of the clunk. He said the noise was actually coming from the rear not the front.
When I got back to the SLC I took it to an awesomely awesome Jeep shop to see if they could figure it out. What we did was a technician got under the Jeep and I got onto the rear bumper and started rocking the Jeep back and forth until we could all hear "clunk, clunk, clunk". The nut job from LJS turned out to be correct, the noise was coming from the rear. It was the rear control arm bolt loose on the pass side. The tech said it's a common problem with Jeeps that are used offroad, rocks hit the bracket and they mushroom causing the bolts to loosen.
The point here is it's very hard to localize a noise from the drivers seat in a unibody vehicle but if you have a willing friend, the same diagnostic proceedure used at the Jeep shop could be used to verify location.
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2006 CRD
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