you can DYNAMAT the vibrating part(s)

Dynamat is your best bet.  I don't know all the specifics about sound
frequency but bass causes soundwaves that vibrate your car and the car is
held together by screws.  Over time the vibrations loosen the screws and the
metal/plastic that got loosened vibrates together making the rattling you
are hearing.

In addition to other ideas, keep in mind that all things have a resonant
frequency, where they get "excited" by noise at a specific frequency.  (For
example, tonearms on  your turntable have a resonant frequency.  They try to
keep the r.f. below anything that will be on your records, because when that
r.f. plays, your tonearm will start wobbling like crazy.  If the r.f. of the
tonearm is 10, that's fine.  If it's 60, that's really bad.)  If your car
stereo happens to be playing bass too loud at some particular frequency that
is the resonance for some part of your car, you'll have trouble usually.