Skype has announced the reason behind the recent outage. The cause was Windows, well more specifically it was due to
“a massive restart of our users’ computers across the globe within a very short timeframe as they re-booted after receiving a routine set of patches through Windows Update.”
After the Windows Updates were run and the computers were all rebooting Skype had a large number of log-in requests and also a shortage in the peer-to-peer network and those both had a huge impact that caused Skype to go down and stay down for about two days for most users. Skype had stayed down because of a bug in the software that prevented the software from self correcting, this bug had not been seen before.
The good news is that Skype is back up and running as good as ever and that this downtime was not caused by any malicious activity so no user data was ever at risk.