I feel for you.
Exactly the same thing has happened to my MacBook Pro, and it is SOOO annoying.
My external mic has been working perfectly for over 4 months (that's how long I've owned the machine), and by co-incidence after the latest update from Apple (that I ran over the weekend, I've not updated for a while before this), the external microphone when plugged into the audio-in socket has stopped working.
I can't believe that it is co-incidence that so many Mac users are having exactly the same hardware fault at exactly the same time (I've seen a few stories like this around the internet), so by conclusion I'm thinking it's the update potentially causing the fault.
I've re-installed OS-X, and reset everything to ensure it's not a configuration issue. The only thing I can't do is roll back the firmware to the previous version, unless anyone knows how to do that?
<Edited by Moderator>
John!