Found this guide on another forum, and given the slew of recent threads on troubleshooting noise, thought I would post it here. One word of warning is that some HEAD Units and/or processors nowadays have a zero bit mute, which essentially cuts off the output during low signal passages to reduce noise.....so be aware if this is a feature your unit has. Onward to the guide;

How can you eliminate alternator whine in a car audio system?

If you have alternator whine in a car audio system and want to get rid of it, there is only one sure-fire way to do it. David Navone and Richard Clark from Autosound 2000 in the USA developed the following step-by-step instructions. If you follow the instructions EXACTLY, you are guaranteed to trace and eliminate the noise in your car audio system. Don’t miss a step and don’t assume that something is OK without checking it.

Each time you check for noise, you should do it with the engine running at 1500 to 2000 rpm and the headlights on full beam so that the alternator will be charging. The tests with the CD player connected should be done with a ‘zero bit’ track playing and the volume at maximum. Set your CD player to ‘repeat’ if it has that feature.

Safety. Make sure when doing noise tests that the parking brake is on and working, and that the vehicle is in neutral or ‘park’. Perform these tests in an area with good ventilation or use an extension hose on the exhaust to route the fumes outside.

Step 1. Check the Amplifiers

1a. Unplug the RCA cables from the amplifier/s and mute the signal at the input by using shorting plugs. This will isolate the amplifier from the rest of the car stereo installation. You can make shorting plugs by taking cheap male RCA plugs and soldering the centre and outer terminals together. This shorts out the input of the amplifier/s to ensure that it has zero signal.

Has the noise gone?
Yes. Go straight to Step 2. Reduce The System.
No. Go to 1b.

1b. Disconnect the speakers from the amp and connect a pair of test speakers to it. Make sure the test speakers are not in contact with the car body. The purpose of this step is to ensure proper isolation of the speakers and the speaker leads from the car's chassis.

Has the noise gone?
Yes. Check speakers, speaker leads and passive crossovers for proper isolation from the car's chassis. Shift passive crossovers to a location away from power cables and the car’s body.
No. Go to 1c.

1c. Isolate the amplifier from the chassis of the car. There must not be any electrical contact between the car's chassis and the amplifier, except for the grounding point.

Has the noise gone?
Yes. Reinstall the amplifier isolated from the chassis of the car. Make sure that the amplifier is grounded in just one point.
No. Go to 1d.

1d. Supply the amplifier with an isolated power source, for example an external car battery or a 12-Volt DC power supply.

Has the noise gone?
Yes. Noise is entering the amplifier via the power supply, try changing the grounding point and add external power supply filtering. Consider changing the amplifier.
No. The amplifier has some severe problems, is totally isolated and still noisy. Replace it or have it repaired.

That is the end of Step 1. You have now either eliminated the amplifier and speakers as a problem or you have replaced a faulty amplifier. Now you can go on to Step 2.

Step 2. Reduce the System.

2a. The amplifier is known to be OK. It is now time to disconnect any signal processors (equaliser, electronic crossover, etc.) and connect the signal from the output of the head unit directly into the input of the amplifier.

Has the noise gone?
Yes. The noise source must be either one or more of the processors or possibly the signal route. Go to Step 3. ‘Add Signal Processors’. If you didn’t have any signal processors and you are using the signal cable in its normal, installed route then the problem is solved.
No. Go to 2b.

2b. Run new signal cables over a new route between the head unit and the amplifier.

Has the noise gone?
Yes. Permanently route the signal cables in the new route. Go to Step 3. ‘Add Signal Processors’. If you don’t have any signal processors then your problem is solved.
No. Go to 2c.

2c. Isolate the case of the head unit from car's chassis. There must not be any electrical contact between the head unit and car chassis except for a single grounding point. Beware of antenna grounds and pullout cases!

Has the noise gone?
Yes. Reinstall the head unit isolated from the car's chassis and any other metal parts in the dash. Ground the head unit at one point. Go to Step 3. ‘Add Signal Processors’. If you don’t have any signal processors then your problem is solved.
No. Go to 2d.

2d. Move the head unit ground to a quieter grounding point. Test a number of points and also try grounding the head unit to the same point as the amplifier.

Has the noise gone?
Yes. Reinstall the head unit using the quiet grounding point. Go to Step 3. ‘Add Signal Processors’. If you don’t have any signal processors then your problem is solved.
No. Go to 2e.

2e. Move the head unit as near to the amplifier as possible. Then connect output of the head unit to the amplifier with the shortest possible RCA cables.

Has the noise gone?
Yes. Reinstall the head unit one step at a time. Check for noise after each step during the reinstallation. Once you have the head unit installed, noise free go to Step 3. ‘Add Signal Processors’. If you don’t have any signal processors then your problem is solved.
No. Go to 2f.

2f. Supply the head unit with an isolated power source, for example an external car battery or a 12 VDC power supply. Make sure that car chassis is not in contact with the head unit.

Has the noise gone?
Yes. The head unit is sensitive to noise in the supply voltage. Add power supply filtering to the supply voltage for the head unit or use an isolated power supply. You may be better to change the head unit. Once you have a head unit installed noise free, go to Step 3. ‘Add Signal Processors’. If you don’t have any signal processors then your problem is solved.
No. There is a serious problem with the head unit. Go to Step 4 'Check the Vehicle' and/or change the head unit.

Step 3. Add Signal Processors.

At this level the amplifier is known to be good. The car's electrical system is OK and the reinstalled head unit is working fine when connected directly to the amplifier.

3a. Connect one of the Processors back into the signal path.

Has the noise gone?
Yes. Go to 3a for the next processor. If there are no more processors, the problem is solved.
No. Go to 3b.

3b. Run new signal cables over a new route between the Head-unit and processor and between the Processor and the amplifier.

Has the noise gone?
Yes. Permanently route the cables on the new quiet path. Go to 3a for the next processor. If there are no more processors, the problem is solved.
No. Go to 3c.

3c. Isolate the processor from the car's chassis except for a single grounding point. Connect the processor ground to the same grounding point as the head unit.

Has the noise gone?
Yes. Provide isolation between the Processor and the car's chassis and permanently route the cables on the known quiet path. Go to 3a for the next processor. If there are no more processors, the problem is solved.
No. Go to 3d.

3d. Since new cables and re-grounding does not help, it is time to relocate the processor very near the amplifier. Connect the output of the processor to the amplifier with the shortest possible RCA cables.

Has the noise gone?
Yes. Reinstall the Processor one step at a time. Check for noise after each step in the reinstallation. Be careful when routing the signalcables. Remember that the car's chassis is a conductor. Go to 3a for the next processor. If there are no more processors, the problem is solved.
No. Go to 3e.

3e. Power the processor with an isolated power supply. Do not let the processor touch the chassis of the car.

Has the noise gone?
Yes. The processor’s power supply in not sufficiently isolated from its audio circuitry. Either replace it or consider the permanent installation of an isolated power supply (1:1 DC/DC converter). This type of device provides a permanent power source that is well isolated from the car's chassis. Go to 3a for the next processor. If there are no more processors, the problem is solved.
No. Go to 3f.

3f. Physically separate the processor and the isolated power supply from the rest of the system by many metres. Use long signal cables.

Has the noise gone?
Yes. Something is seriously wrong with either the processor or your install/test procedures. Please repeat this level from the beginning.
No. Change Processor -- this one has design problems. Go back to 3a for the new processor.

Step 4. Check the Vehicle

The suspect car's charging and electrical systems can be checked by using the previously installed sound system in a "known quiet" car.

4a. Connect jumper cables between the batteries of the two vehicles and start the engine of the suspect car. Turn on the headlights on the suspect car and listen to the stereo on the "known quiet" car.

Is there now noise in the quiet car’s system?
Yes. Have a qualified auto electrician check out the car’s charging system.
No. The suspect car's alternator and charging system is now proven to be quiet. The problem must lie in the car stereo installation -- not in the vehicle.