I'm assuming its not the factory radio, but do you have an amp in the car running the speakers? I'd check your grounds, and if that doesn't fix it then try the RCA's running to the amp if you have one, and if that doesn't fix your prob then the pre outs in the radio are bad. Other than that I have no idea what it could be
Mine does it when I have my iPod hooked up through the FM modulator. When ever I accelerate the humming gets louder and slows down when I do. That sh!t's annoying. Usually turn it off and listen to the exhaust note. That also gets louder when I accelerate and stuff, but it's supposed to.
Have you had the heads or engine out? There are two small gray plastic boxes bolted to the rear of each head by the firewall (one on each). They are capacitors to keep RFI down.
Also, if you are running colder range non-resistor sparkplugs, you will get noise. Try a resistor plug.