Hackaday has a few tips on adding an auxillary jack to your car stereo as a direct input for you iPod or mp3 player of choice.

Some car stereos (aftermarket) come with line-in jacks on the front of them. If you happen to still have a stock head unit, there are a few tricks you can use, from soldering the jack on to the board, to repurposing the connection for an external CD changer.