Phil Zimmermann, the creator of the popular public key encryption application PGP, has released a public beta version of Zfone, a free utility for encrypting Voice over Internet Protocol (VoIP) communications that use the SIP protocol. It is available for Windows XP, Macintosh OS X, and Linux:
http://www.philzimmermann.com/EN/zfone/index.html
To use Zfone, you'll also need to use a SIP-compliant VoIP application. I'm currently using Gizmo Project, Windows, Macintosh, and Linux versions of which which may be downloaded free here:
http://www.gizmoproject.com/
Zfone encryption has an advantage over Skype's in that Zfone generates unique, single use keys for encrypting each conversation. Keys are not stored on a server run by a central service, as with Skype. While the FBI might be able to serve eBay (Skype's U.S. parent company) with a National Security Letter (http://en.wikipedia.org/wiki/National_Security_Letter) demanding a customer's encryption key, no such thing can be done with respect to zFone. See the Zfone FAQ for more:
http://www.philzimmermann.com/EN/zfone/index-faq.html
If you would like to try out Zfone with Gizmo, you can reach me at my Gizmo user ID: georgemaschke.