I had what sounds like the same problem and somehow either updating to the latest software (yosemite as of now) and/or opening up dictation and speech has fixed it for now. I have no idea why. But if anyone else has this problem you might as well try it if you haven't already.
I was on skype with a friend, hung up, went to go do something else without moving my laptop at all, and then when I tried calling him again when I got back he couldn't hear me at all. I went to sound under settings first and it couldn't pick up my voice at all even though input volume was on full blast, but it could pick up if i tapped the mic with my finger. So I looked around the internet and did an smc restart, messed with terminal, messed with audio midi setup, made sure nothing was on mute. I didn't have any other mics to select other than the default so I couldn't switch that around. Finally I decided to try the free upgrade to yosemite. At first it still didn't work but then I randomly opened up speech and dictation under settings and it was all working perfectly again and I could talk on skype. BUT when I opened up sound prefs again it stopped working. Opened up speech and it was working again. Perhaps somehow those two panels turn something off and on? Very strange. Anyway I hope this isn't too incoherent as my coffee still hasn't kicked in yet but I hope this helps someone and maybe someone knows why this could work.