Most aftermarket head units have inputs in the rear whether via RCA jacks or whatever it may be. Connecting an iPod should be as simple as getting the proper connectors or adapters from radioshack or your favorite stereo equipment source. For example, you can get an RCA-to-stereo miniplug Y-cable such as
this to directly connect your iPod to an aftermarket head unit with RCA inputs in the rear.
Unfortunately, hardly any factory-installed head units have such inputs. If you have your original factory radio, you have several options:
1. Use an FM transmitter such as an iRock or the soon-to-be-released iTrip. Works well but sound quality is not very good compared to other wired options. Sound quality is acceptable at best.
2. If you have a cassette player, use any of the many available adapters. Sound is much better than any FM-transmitter and is considered very good by most people.
3. Do your research on who's the manufacturer of your factory head unit and track down where you can get a special harness that will provide you with audio inputs to your factory stereo. Check autotoys.com or crutchfield or your local car audio specialist for more info. This may be the only option for audiophiles. The best possible sound quality you can get from iPod connectivity.
4. If you have a CD-changer, you can ditch that and find a harness that will turn the CD-changer connection into a generic audio-input. This will only work with certain cars and certain model years. Personally, I can confirm that this route is possible with audi and volkswagen factory head units from model years 1999-2001. I bought my harness plug for $60 from autotoys.com. Sound quality is the same as (3).