Maybe a loose screw or broken clip on the door panel. Do you know if the door panels have ever been removed?
To update on my car- it now has 231K, with minimal interior noise. When I first got it at 224K- it was 100% rattle and squeak free. Now, when I hit a big bump, if my front passenger side window is down, it will "rattle" in the door. I still get the occasional "tick" or "pop" sound when I hit a sharp bump, but the car is 14 years old and it has endured 14 years of sunshine, so I am sure many interior parts have shrunk. Still, for a 14 year old car, with 231K, it is impressively quiet, except for the front suspension "clunking" when I go over bumps.
To answer another question - yes- driving on rough roads will make a car rattle sooner than normal.
I have a 98 LS. In the past when i was waiting for the traffic light, I heard the sound from the front passenger's box(under the CD charger). I could stop it by open it & close it immediately. However, it happened again for the next traffic light. About 2 weeks ago, I have my dealer replaced the engine mount & Tranny mount. All of this was gone. Also, it is incrediable that the engine is super quiet & just like I'm driving an electronic car. I hope this helps.