(via http://www.reddit.com/r/worldnews/comments/1o7zfr/skype_under_investigation_in_luxembourg_over_link/)

• The NSA was offering billions to anyone who offers a reliable eavesdropping solution for Skype. ¹⁾
• Microsoft buys Skype for $8.5 billion, more than twice what Google or Facebook were offering. ²⁾
• A month later, Microsoft was granted a patent for a “legal intercept” technology designed to be used with VoIP services like Skype, which enables silently copying communications transmitted through them. ³⁾
• MS moved Skype's supernodes to its own in-house data centers, getting rid of the decentralized P2P architecture of Skype (which was hindering eavesdropping).⁴⁾ and ⁵⁾
• MS continued to state that the move to this new architecture is to ensure stability/reliability of the network. ⁶⁾
• However, they continue refusing to comment on whether they eavesdrop on the communications, and their ToS/privacy policy make no guarantees about this. ⁷⁾
• MS buying Skype for a whooping $8.5 billion, makes it a telecommunications carrier. And under CALEA, “telecommunications carriers and manufacturers of telecommunications equipment are required to modify and design their equipment, facilities, and services to ensure they have built-in surveillance capabilities, allowing federal agencies to monitor all telephone, broadband internet, and VoIP traffic in real-time.” ⁸⁾

• Skype developed a backdoor access system for the NSA before the Microsoft acquisition as part of a secret project involving only a dozen people and created by the government.⁹⁾
• Report: Skype Formed Secret “Project Chess” to Make Chats Available to Government ¹⁰⁾

What should I use then?

An alternative for your IM/VoIP needs is Jitsi. It's open source, supports every popular protocol, and out of the box full end-to-end encryption (uses OTR for instant messaging encryption and SRTP and ZRTP for XMPP and SIP encryption).