There are a number of Ipod interfaces that make the Ipod mimic the CD changer. To use the Ipod you have to create playlists that are named EXACTLY what the interface is looking for, usually something like CD1, CD1, CD3, etc. Then the stereo deck thinks it is talking to the various CDs in the changer. It works, but you can't randomly search for songs or play anything that wasn't in a play list.
There are stereo decks that have a dedicated IPOD interface that works much better. Alpine, Kenwood and I believe Pioneer have them, and there might be others as well. I installed an Alpine CDE-9845 in a car and it is awesome! The Ipod is stashed away in the glove box and I can control all the Ipod functions through the Alpine head unit: title search, artist search, playlists, shuffle, etc.
If Alpine had a wired remote I would install it in my boat in a heartbeat!