I have narrowed my drivers door rattle to the piece of plastic that covers a small section behind the area where you pull the door to close it. Mine rattled only when driving over rough roads. I have a rattle from the left side some where, where, oddly enough, only presents itself when its the first time driving of the day, and when my daughter is in the backseat when I am driving her to school.
Weird. Also have some sort of slight vibration rattle from the center of the dash, again only happens with rough roads. Now that I have SLP knockoffs it seems to present itself more often now.

 

Oh, and I just removed those plastic door inserts, we'll see if that takes care of both doors.

 

I had the same rattle behind the door handles. Took 'em off, applied stick-on thin weatherstrip, and popped 'em back in. No issues since.