To keep my stereo looking stock, I wired an aux input to the stereo and hooked up an ipod nano. The ipod has rockbox installed on it so it automatically starts and shuts down with the stereo.
To keep the ipod hidden but accessible I mounted it in the centre console compartment. To mount the ipod I bought a bag of iphone cases and carved them to shape as per the pictures. I used auto putty to fill the gaps. The dock permanently holds the nano and lets me drop the iphone on top.