I've tried using Banshee, Amarok, and Rhythmbox, and so far I've been unable to set the "Remember Playback Position" property of some files. In iTunes this was done through the "Get Info" menu but I don't see any way to do this in the aforementioned programs. How can I do this with Ubuntu?
You probably will have to use iTunes to use this specific feature for an iPod. The feature isnt available through the apps you have mentioned.
This isnt the same as setting "Remember Playback Position" for every individual track as can be done via iTunes, but the following SU link discusses creating a python script to remember a specific point in a playlist: http://superuser.com/questions/249565/music-player-for-linux-which-remembers-the-playback-position