From some instrumental recordings I've done using my laptops internal mic, I knew that it has quiet a lot of background noise. What if that noise is transferred to the other persons speaker, amplified, fed back into my speaker, fed back into my mic again and added to the background noise it produces already, back to the other persons speaker and back again creating an unstable positive feed-back loop?
The theory was easily proved in practice. By using head phones, the feedback loop was broken and the high levels of noise disappeared.
The software engineers at Skype could probably have good use of the noble teachings of Nyquist to get rid of this. I bet though that a simple noise gate could do the trick. There is one such avaliable online as a plugin but Skype hasn't incorporated that in to their software yet as standard.