I have a 3G iPod and there is a line out on the dock. I also have the the Altec Lansing inMotion speaker set and there is a line out connection on the back of that as well. I imagine the better sound might have something to do with the signal being line level, versus powered for the headphone jack.
Given how common 'pods are becoming in set ups - if only for convenience - good thread idea. But probably in a different forum.