Aux input is definitely FAR superior to FM transmitter OR tape adapter. those options are just way too noisy for even an undiscerning ear, and the frequency response is pretty poor, especially for FM.
That being said, you don't actually need a head unit specifically with aux inputs. Anything that can support an external CD changer will work, too, you just need an adapter to convert the audio inputs for the CD changer to normal RCA's (available at installation), then either a stereo-mini to RCA line for the iPod or (i recommend) one of the
Belkin auto adapters that powers the ipod and sends audio via a stereo mini (ie. "normal headphone) plug. Although, I rigged my car so that the DC power comes from the floor of the passenger side, and the stereo line goes into the console from underneath, so all I have is an iPod (mounted to the side of the head unit) with a single white line going straight down
Of course, something like this:
Alpine iPod head unit would be sweet but probably expensive.
Anyway for the head unit I bought
this and couldn't be happier (got it for around $160 using a friend's discount -- you should be able to find online somewhere for around $180 or so). For my full review of it click
here. It's kind of old now I guess, so shop around you'll find something better, probably.
EDIT: I certainly do NOT mean to endorse any of the stores I linked to for purchase -- just used them for informational purposes. Hunt around and you'll find better deals for all the linked products, which are just personal recommendations based on satisfied use. I don't really know anything about the Alpine unit, but I imagine it's pretty awesome, just wanted to include it as an example of what's available (or coming soon).