We've heard these noises before too, and have no clue what is causing them. It isn't snowing, or windy, nor are there any trees near where the banging is happening. And it is really loud and strong - it kind of shook my floor a little once, and sounds like it is almost cracking the roof. It's like a 300-pound man is jumping on the roof. I wouldn't think that there would be any sort of repairpeople up there at midnight on a Sunday night, nor is the roof easily accessible to any pranksters - it would require putting up ladders and whatnot, which would be kind of obvious.
Any ideas as to what is causing this?