While not iPod specific, I've been living with a CarPC running Streetdeck now for about a year, and there are a few key things I miss about the empeg:

• The prefer/dislike artists/album feature where I can either queue up more songs from the same artist real fast, or remove them from the current running order
• Marking tracks for attention
• Hierarchal organization of my music
• Easy to add songs due to the pullout design, something an iPod solution would do as well
• Auto volume normalization
• Quick, reliable and dependable resume from sleep/powerup sequence
• The use of an internal master playlist that allows me to queue up a bunch of music, hit shuffle, and listen from start to finish with no duplicates
• Bookmarking, to allow the saving of the above mentioned playlist if I want something else for a short time

Most of these features are unique to the empeg, and have not been duplicated into the iPod design. I'm assuming most head units are limited by what the iPod can do.