I was able to fix it by installing the gnome-alxamixer package and
checking a "rec" checkbox under "Capture". This must have been unchecked
somehow by some application. The strange thing was the no option in the
gnome-volume-control or any other standard location allowed me to fix it
or even track that.

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[ubuntu karmic] no microphone in skype
https://bugs.launchpad.net/bugs/437192
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