With a Sony CD/MP3 head unit, and a device called the RetroRadio, you can continue to use the hand controls. I installed this on my FLHTI this past summer, and it works great! Not cheap though, the RetroRadio itself is about $200, and then you have to buy the head unit on top of that (and speakers). I ended up paying about $500 total, including the antenna (have one inside the fairing).
It sounds great though, and it's nice because the Sony units automatically adjust the volume based on speed (mine does at least). Not sure if the H-D units do this or not, but it's a nice feature to have on a bike.
The RetroRadio is made by BikeTronics, Inc. There are a few other makers out there that I've heard good things about too.