On the drive home from the gym this morning I began to hear a thumping coming from one of my tires. I checked for an idiot light and saw nothing. Then I began to suspect a large stone in my tread. Sure enough, a pebble about the size of an acorn was caught in the center of the tread. Since the tires are much harder than traditional tires the stone made much more of a racket (I could feel it in the steering wheel as well) than I thought it would. So if you hear the same thing, don't freak out like I did, just stop and look for stones.
Heh, that happened to me a couple months ago. It was a little pebble from driving through road work. Felt kind of silly for being worried after I found it.