If you are under warranty, definitely take it into the dealer and let them take care of it, or diagnose what it is, at the minimum.
With that said, I think it's important to try and determine the general vicinity (sp?) of where the clunking is coming from and the specific conditions. The reason for this is that I had a strange clunking noise start to show up a few weeks ago. It was really only noticeable over bumps. Over time it started getting louder and louder to the point where I knew something had to be wrong. Driving with the windows down, I was able to pinpoint it to my right rear suspension area. I parked the car, opened the trunk and started pushing down with my hands on the inside of the trunk to make the back of the car bounce. That really made the right rear clunking very noticeable.
I took it to a shop and they discovered that the bolt connecting my right rear strut to the control arm was rusted out and broken. It was at the verge of completely snapping in half. In fact, the mechanic managed to break the head of the bolt from the threads while removing it. He came and showed me the broken bolt and told me I was extremely lucky I made it to the shop before it broke completely. He noted that it was extremely rusty (despite my car only having 35k miles and always being parked in a garage each night). He checked the others and replaced them. Needless to say the clunk is gone after replacing that bolt (an the others, proactively).
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