This article is from the Car Audio FAQ, by Ian D. Bjorhovde (firstname.lastname@example.org) with numerous contributions by others.
The amps have been determined to be noise free. If you have any
processors between the head unit and the amps, disconnect them and
connect the head unit directly to the amp. If this gets rid of the
noise, then one (or more) of the processors must be at fault, so
proceed to level 5. Otherwise, try running the signal cables over a
number of different routes. If you are able to find one that does not
produce any noise, permanently route the cables in the same manner, and
proceed to level 5. If not, then you must isolate the head unit from
the car's chassis (except for its ground!) - don't forget to disconnect
the antenna, since it is also grounded to the car. If isolating
the head unit does not solve the problem, the move the grounding point
of the head unit. Hopefully the noise will be gone, and you can
install the head unit with a quiet ground and proceed to level 5,
otherwise go on to level 3.