Best thing I bought was a new deck (alpine) with a direct input specifically for iPod. It hooks into the dock connector at the bottom of the ipod, and with the deck I bought you could control the iPod through the deck. So in other words you just put the ipod in the glove box and leave it. Always charged, always reliable.
you can probably get some sort of a deck/ipod cable for under 100 online now...i bought a really good one, as i hooked up satellite radio etc to it, so it was a bit more $$$...
As for the previous person suggesting an AUX-input thing...yeah, that's probably the second-best option. It's of course lower sound quality than what I suggested, but much better than an FM transmitter (don't waste your money on this crap)...other issues to consider with the AUX-input things are that you have to constantly charge, and that you can use the volume on the iPod. I personally don't like having two volume controls...
If you've got an aux-in on your current deck, just buy a cable to hook the ipod up through that, its only a dollar or two...if you've gotta buy a new deck, i would suggest getting an ipod compatible one, just don't get an FM transmitter...