Other than a "critter" of some sort, the other thing that comes to my mind when you describe the noise is something to do with the water pipes. The reason I say that is...once I lived in a house where noises like this started occuring, and it was finally traced to the water lines. (loud thumps, short bursts of vibratory sounds similar to a jack hammer, etc.) I think they called it "water hammer" or something like that. It just happened occasionally. Was especially unnerving when it happened in middle of night! Anyway, that's my story and I'm stickin' to it.
Keep us posted!