Assuming you are concerned about the code you run, the location you run it in, etc. Does not provide encryption to my knowledge, but VPN can solve that.
I don't know of any truly distributed encrypted voice systems you can trust out there. Hosting your own server for a service seemed like the next rational way to solve the persons question.
Try not to think in terms of server and client being separate machines. Or thinking that a server needs to be complex or able to handle an unlimited number of nodes. It's possible to be both a client and a server. And that is in fact what Skype was doing. Some clients were also functioning as supernodes.
Teamspeak is another option, along the lines Mumble. There are others. It's a diferent concept from Skype. ONe person has to run a server. They choose who they want to be on the P2P network. Teamspeak is closed source.
Free SIP services are another option, but not easy enough for the novice who is in a hurry and just want things to work. Most people seem to use SIP servers operated by companies, not running the servers themselves. Some ISP's are selling pre-packed VOIP service (and some are deep inspecting every packet, lol).
Skype has the market now. It is ubiquitous. It's easy to use and works reasonably well.
But to think Skype will become the world's new default global communications channel, with MS in control, is just silly.
Skype is just a hint of what's possible, given today's bandwidth and a network that no one player controls.
Assuming you are concerned about the code you run, the location you run it in, etc. Does not provide encryption to my knowledge, but VPN can solve that.
If you are looking for something more robust that can interconnect with telecom stuff, I'd suggest http://www.freeswitch.org/ or http://www.asterisk.org/