I can never work out how to get Skype to play nicely with pulseaudio on Debian/Ubuntu. So blow away pulseaudio and use alsa instead:

sudo killall pulseaudio
sudo apt-get purge pulseaudio pulseaudio-utils gstreamer0.10-pulseaudio  paman pavumeter pavucontrol
rm ~/.pulse-cookie
rm -r ~/.pulse
sudo apt-get install alsa-base alsa-tools alsa-tools-gui alsa-utils alsa-oss alsamixergui libalsaplayer0

One day I’ll work out how to get pavucontrol (?) to do its thing, or Jack, or whatever.