If you're calling from computer to computer, you shouldn't need a service like Skype. VOIP providers help you make calls to non-VOIP phones if necessary, but you should be able to "call" from one computer to another just using audio encoding and IP packets. And you should be able to encrypt it from end to end.
Do any of you already use desktop software like this?
The reason almost everybody uses a vendor like Skype that they solve the problem of helping users find each other and establish connections, despite NAT and firewalls.
I don't know of any non-commercial, distributed software for solving that problem.
WebRTC provides this directly in-browser via a javascript API. It works right now in the latest version of chrome without any special flags, and also in the latest stable firefox if media.peerconnection.enabled is turned on.
This is capable of sending multiple video/audio/data streams directly between two browsers even if they are behind a NAT router.
edit: Sorry i misread your post. WebRTC does not solve the user discovery problem but any other web tech can be used for signalling anyway (AJAX/EventSource/Websockets)
Also, there is already a SIP implementation built on this API
Do any of you already use desktop software like this?