Okay well we all know that Art Marvelous is the expert here
but I will give you my diagnosis.
You are picking up ground noise, First is your stereo, amped (factory or aftermarket), what are you using for a ground if it is. Does your power come factory from the fuse box, or are you pulling power from one of your two batteries, if aftermarket amp where are your RCAs run and how old are they, what about your remote on wire. Also does the noise come from all speakers or one? You mention the cig lighter and xm/ipod, are you running these with a fm frequency or direct connection?
Start there and let me know.