This article is from the VW Technical FAQ, by with numerous contributions by Jan Vandenbrande others.
A: VWs are unfortunately well known for this. Part of the cause is the rather
stiff suspension and hard motor mounts that just rattles the car apart.
Often the fix is easy once you find the cause. The following are a few
tricks that I have used over the year that will help eliminate a good deal
of them.
Tip: Start with cleaning the inside and outside of the car, and remove all
the coins and pens stuck in the seat rails. Then take a screw/nut driver
and fasten all accessible interior screws and bolts. If a particular
screw/bolt loosens frequently, use Loctite (tm). The bolt that holds the
seat back adjustment knob is notorious for loosening and rattling. Have
someone drive around while you go around and isolate where all the noise
comes from.
Another weird one that helps with some rattles and groans is to install a
lower stress bar on A-1 cars that do not have one, and apparently an upper
shock tower stress bar on all others (haven't tried this yet, but Aaron @
APS claims that it helps surprisingly well).
 
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