Are you buying this thing to listen to music, or are you mostly interested in being seen with it?
A white iPod will hide the scratches better, will be easier to see and retrieve if you accidentally let go of it during a space walk, will more conspicuously show that you've got one of the hot new electronic items from four years ago, and will retain its appearance if you accidentally drop it into a sack of flour.
A black iPod will most likely look better in a car (most have at least some matching trim) and stand out slightly less to thieves, but it will show the scratches more easily and stands a much better chance of getting lost in space (you may get lucky and have the shiny back showing, so don't let this issue be an overriding factor in your purchase).
You could ignore the practical considerations, of course, and simply pick the color you like better.