Adrian Game’s iPod Accessory Serial Protocol page and iPod Linux have great information on the commands and the structure used to send instructions to iPod. This is not Arduino specific.
Rosie Daniel’s blog has information on controlling the iPod remote with Arduino. This is great if you’re wanting to use the “basic” iPod functionalities, namely play/pause, next, previous, volume up, and volume down.
The instructions from the Arduino to the iPod are all going to happen in hexadecimal so you might want to familiarize yourself with the way it works. This translator often helped me put the instructions into perspective.
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