I had the following problem on the macbook pro 15 with retina: when i plugged in a 3.5 mm headset, it replaced the microphone in the sound settings in the system preferences as the audio input. but I wanted to use the built-in microphone, as my headset broadcast my computer sounds in Skype calls and built-in mic was much better than headset. I've googled a lot and found on this forum similar issues and didn't find solutions. But invented it myself: I plugged the headset in 3.5 mm extension, which transfers only the outgoing sound. most of the 3.5 extensions work so: only 2 channel output. Mountain Lion don't identify headset as headset, but as headphones and built-in microphone is not replaced with external. I hope this helps someone.