I had this problem in 10.04 and it was solved.
pavucontrol was the solution the last time, I muted one channel and the microphone worked then. But now in Ubuntu 11.04 I have to change both channels at the same time. as the screenshot shows.
So here is my problem.
I can't use my built in microphone in skype, but in windows I can.
skype -version gave: Skype 188.8.131.52