Update: I wrote this entry a long-long time ago, the problem is probably gone, or you need a different solution now...
Now that I've benn using Ubuntu for a few days, some usability problems appeared. The most severe is that the Skype icon on the icon bar doesn't indicate new messages in a clear way. The solution was to install an indicator for skype:
sudo add-apt-repository "deb http://archive.canonical.com/ $(lsb_release -sc) partner"
sudo apt-get update
sudo apt-get install skype && sudo apt-get -f install