trouble shoot the problem - don't guess at it.

describing the wirring sound more - does it only happen with the engine on or at all times? does it varry with engine RPM.

you can run power and RCA on the same side of the car - I bet if most of you pulled back your best buy/circuit city installed systems, you'd fine them run this way. It's not recommended, but it's not a guarentee of noise. If this was causing an issue, the problem would be with teh subwoofer making noises, and 99% of the time you can remedy this with a good ground.

The thing that troubles me is that 1. the rear speaker is powered off of the head and 2. it only happens in the right speaker.

This points to it not being a ground loop issue. Where exactly is the amplifier grounded?

I'd be inclined to think it's something with the wiring of the headunit.

Step one is to disconnect the sub/amplifier combo from the system - then listen - if the noise goes away, then it's an issue with the amplifier - somewhere you botched the installation/setup.

If the noise doesn't go away, swap speaker leads at the head unit for rear right and left. If the sound travels over to the left speaker, then it's something in the headunit, if it stays on the right side, there's apinched wire or an issue with the speaker itself.