If I recall correctly Skype was working with the NSA before it was acquired by anyone.
Wrong. Skype was bullet proof, completely end-to-end encrypted, before the MS takeover.
Before Skype was acquired by Microsoft, several news articles suggested that it was possible for Skype to allow governments to monitor conversations.
http://www.h-online.com/security/news/item/Speculation-over-...
But yes, if you made sure neither computer had NAT and used no super nodes it was possible to be pretty protected (except for the problem that PRISM is tied to the network hardware and can read anything anywhere on the internet).