I have a 2005 model Pioneer deck in my car, and opted for an adapter that accepts an audio RCA composite red/white input. Most aftermarket decks offer an iPod adapter, usually at the expense of around $90-$120. With the 2005 Pioneer decks, the Pioneer iPod adapter allowed you to control your iPod from the actual deck, without ever touching the iPod itself. In theory, it was excellent. In practice, however, was an exercise in frustration. Hell, you had to go through a couple of menus just to fast forward or skip tracks. With the 2006 Pioneer models, however, all is well, and the adapter works just beautifully with the deck, with minimal fuss.
I think Alpine's solution is pretty good also, but haven't read much up on it.
If you can, go for any option other than an FM transmitter or tape-deck adapter. The quality is just crap. Plus, for the money you'll put towards a decent FM transmitter, you might as well put the same or a bit more money into a better solution.