For instant messaging and online phone or video chats, you can avoid Microsoft and Google services like Skype and Gchat by adopting more secure alternatives. Jitsi can be used for peer-to-peer encrypted video calls, and for encrypted instant message chats you can try using an "off the record" plugin with Pidgin for Windows users or Adium for Mac. Like using PGP encryption, both Pidgin and Adium can take a little bit of work to set up — but there are tutorials to help ease the pain, like this for setting up Adium and this tutorial for Pidgin.
As for phone calls, if you want to shield against eavesdropping or stop the NSA obtaining records of who you are calling and when, there are a few options. You could use an encryption app like Silent Circle to make and receive encrypted calls and send encrypted texts and files, though your communications will be fully secure only if both parties to the call, text or file transfer are using the app. Other than Silent Circle, you could try RedPhone for making encrypted calls or TextSecure for sending encrypted texts.
A new frontier of sweeping secret surveillance is not a conspiracy theory but a burgeoning reality. But it is not an Orwellian dystopia — at least, not yet. Tools to circumvent government monitoring exist and are freely available. The onus is on us as individuals to learn how to use and adopt them.