I have heard that Skype can mute other programs during calls. I would like to configure it to do so automatically.
I use Windows XP and Foobar2000
The best way I've found to do this on Windows is by going into Sound, under control panel (Control panel -> Sound) and then click on the "Communications" tab. There, you should see an option to "Mute All Other Sounds" during a call. This actually works with Skype 4.0+.