I love my Prius, but...
Whenever I try to play my iPod Touch or Blackberry in my 2009 Prius using a charger plugged into the speaker AUX jack, there is a noise that comes through the speakers. This is most likely caused by a ground loop and only happens when a charger is plugged into the Touch or Blackberry.
The Solution
To prevent this from happening, your best bet is to buy a Ground Loop Isolator from Radio Shack. and a Y-Adapter.
How to Hook it up
Once you have your parts from Radio Shack, here is how you hook it up:
A few cords to contend with, but no more noise. One tip: keep the black cylinder part (labeled "Audio System Ground Loop Isolator") away from your charger to avoid additional noise.
Success!
No more ground loop noise! This works great when I'm listening to and charging my iPod or listening to music from by Blackberry Storm while charging.
For Older Prius's, there may be another fix...
If you own an 06-07 Prius, Toyata actually issued a TSB for this problem. You can read about it here.
Check out PriusChat
PRIUSChat is where I originally discovered some help for this problem. Great resource for Prius owners.