I've got an Ipod shuffle and Sirius satellite radio in the WJ. For the Sirius, the unit came equipped with an FM transmitter built in. This worked OK, but faded very often. So, I found out that Audiovox (who made the unit) made an "FM booster", which attaches to the base, and plugs into an "FM out" jack. It then runs to a box which connects to the radio antenna. What it does is send the signal to the box, which in-turn overrides almost all FM signals except the one set for the transmitter, and gives you the same quality sound as plugging it in directly. I like the technology, I wish they made more systems like this.
For my Ipod Shuffle, I haven't used it in the YJ yet, but I've used it a lot on my boat. I bought the cheapest receiver I could find (due to vandalism last year), which happened to be this $29 unit from wal-mart. After I got it home I realized it had a 1/8" Mini jack right on the front. It works great, and for $29, it's the cheapest unit I've ever seen with an aux in jack.
My girlfriend uses her 20GB ipod in her TJ with the Monster FM transmitter/charger. It's OK, but the frequency selection is pretty limited, and the signal isn't very strong. In the interim, she's been using the cassette adapter. She's looking to upgrade to the cradle FM transmitter, due to it's larger selection of transmitting frequencies.