After my iPhone3GS was upgraded to iOS6 I was unable to get the sound of voice calls on my car stereo which is connected via cable to the iPhone using a 3.5 mm jack. Surprisingly the iPod music function worked fine.
I then tested the iPhone with headphone and the same problem occured when I tried to make calls, no sound, but when I selected the play music option up popped the choice of headphones or AppleTV. I selected headphones, and then tried to make a call. It would seem that the upgrade set some AppleTV default. Having unselected Apple TV my problem appears to have been solved. The headphones and car stereo now work for phone calls and music output.