Well a few that come to mind are :

HD space. From what I know about the IPOD you cannot upgrade the 20gig HD at all and it sure doesn't have room
for 2 drives.

Next would have to be options and the display. Empeg is made to operate in the car and its alot more safe.

The empeg is an empeg. There is nothing to compare to it. The only thing the IPOD has over the empeg is size and mobility. Something the empeg wasn't designed around.

Ohh.. and ethernet support. I do believe that is a plus.