[Seawolf]

I have a 2007 Miata that used to do the same thing. There was a tiny screw under the plastic cap on the shifter (the cap that has the numbers printed on it) that had worked itself loose. I pried the plastic cap off, found the screw, and put it back in its hole and tightened it up. I then superglued the plastic cap back down.

Now, I don't necessarily recommend you start prying parts off your car already, but you may be experiencing a similar issue.

Try unscrewing the shift knob (assuming it will unscrew like just about every other shift knob) and drive around with it off. If you don't hear the rattle anymore, then the knob is the problem.