My passenger window rattled when it was all the way down. Before the adjustment I could easily hear the rattle noise when closing the door or wiggling the glass. I had tried tightening the screws at the top of the rails as has been suggested, but they were already tight. (BTW, that's a very easy check and you should start there.)
Read the warning posted later in this thread from TheViper before adjusting these screws:
Window Rattle Fixed
It sounded like the rattle was coming from the glass hitting the aft rail. Assuming clockwise turns of the window angle screw at the bottom of the door would only press the window tighter against the seal when up, I figured it wouldn't hurt to try it.
I turned the screw a half turn clockwise and the rattle diminished. I turned it another half turn and the rattle was essentially gone. I turned another half turn for good measure and called it good.
I may have been a little lucky, but I bet some independent adjustment of the window angle screws will fix this rattle for most people.
-Shawn