Like Tony asked, we need to know your setup.
I have my CDplayer, empeg, and both amps powered directly from a capacitor which is attached directly to the battery. Also, each one of these items has a seperate ground wire all brought back to a single point under a giant bolt in the trunk. I did this from the outset to make sure I had no ground loops, and it appears to have worked.
You might try running extra wires around the car... get a hundred feet of lamp cord and just start trying things - connect each item's power right to the battery. Connect each item's ground directly to the battery. Try running RCA patch cables over top of the seats to any amps that you might have. Basically, run everything like you would on a bench, and see if the noise goes away. Then replace each wire one by one until you find the culprit. This approach has worked for me in the past.
Also, depending on the setup, could you be picking up inducted noise into an RCA cable, possibly by having it run too close to something else? I had a pretty bad noise in my last car until I realized my patchcord ran next to the heater blower motor.
Just some ideas to try.