Only devices in the Made for iPod program which use Apple's proprietary authentication chip can communicate with the External Accessory framework on the iPhone or iPod touch. Such devices must also expose a protocol that iPhone applications can use.
It is a reasonably involved process to be approved as a Made for iPod vendor of products (similar to the App Store approval process, but for hardware), but it has become a lot easier than it used to be. With iPhone OS 3.0, Apple has opened up the program to many more third parties than just the usual large accessory providers.
In your case, I'd actually wait and use another vendor's iPhone-controllable stereo. Manufacturers are just starting to come out with hardware controllable via iPhone applications, so it's only a matter of time before one of the larger accessory providers creates something like what you want. If they expose a protocol for controlling the device, all you'll have to do is write your application to control the device via that protocol.