I had the same type of noise shortly after I bought my 06 last year. It seemed to happen at random times and it was very difficult to pinpoint, as many rattles are. I was convinced it was coming form the sunroof at one point. Then I thought it only happened when I made left turns. It was frustrating as hell. The sound was awful and it had me convinced I was in for a big $$ repair.
It turns out it was a heat shield. If you're not familiar, they are like aluminum baking dishes you might make a turkey in attached at various points on the undercarriage. The one that was making the noise had come completely off and was sitting on top of the muffler so I couldn't see it when I looked under the truck.
I seem to remember it had been attached with 2 bolts and the holes had worn so they were too big for the bolts. It is very possible one bolt could come loose and create a rattle.