I have an Alpine CD unit that will run my iPod.... It's model..CDA 9728... They have 4 units that are iPod compatible I believe. Mine is the second one up the line.. will play WMA and MP3 formated disc's as well.
You need to buy an "adaptor" or whatever they call it... it's an additional $75.. it simply plugs into the back of the deck, you hide the small box, and leave the iPod connection end accessable.
Works pretty well. I don't even bring CD's along with me anymore.