Following my sound issues with Skype on Ubuntu, I did a bit more research and eventually found an excellent how-to article on PulseAudio in the Ubuntu forums. Appendix C explains how to get Skype to work properly and indeed it is a doodle and means there is no need to kill PulseAudio when using Skype! I've tested it in Intrepid and Jaunty and it works a treat. To quote the article, here's how to do it:
Open Skype's Options, then go to Sound Devices. You need to set "Sound Out" and "Ringing" to the "pulse" device, and set "Sound In" to the hardware definition of your microphone. For example, my laptop's microphone is defined as "plughw:I82801DBICH4,0".
You will have to experiment with the different options for "Sound In" until you find the correct one: choose an option, click on "Make a test call" until you find the option that works. On my machine, here's what the option window looks like: