This article is from the Car Audio FAQ, by Ian D. Bjorhovde (firstname.lastname@example.org) with numerous contributions by others.
After you have determined that there is noise in the system, determine
if the amplifier is causing the noise. To do this, mute the signal at
the inputs to the amp by using shorting plugs. If there is no noise,
then the amp is fine, and you can proceed to level 2. However, if
there is noise, then use a test speaker at the amp's output. If this
stops the noise, then the problem is originating in the speaker wiring,
or the passive crossovers. Check to make sure that none of these are
shorting with the body of the car, and start again at level 1. If
noise is still present when using the test speaker, then there may be a
problem with the power supply on the amp. Try connecting an isolated
power supply - if this does not get rid of the noise, then there is
something seriously wrong with the amp, and it should be replaced. If
the noise goes away, then there may be a problem with power supply
filtering or isolation. This can be fixed by changing the amp's ground
point or b adding external supply filtering.