There's a few voice over IP (VOIP) programmes for GNU/Linux:
- Empathy (the default on Ubuntu I believe)
And a few more, but these are the 'main' ones.
Here's a screenshot of Ekiga:
And here's Linphone (link): Linphone Screenshot
They all support using a proxy. I've always used Ekiga, but recently tried out Linphone as it has apps for Android, Blackberry, iOS, Windows, etc. making it a little easier for friends and family who I've not yet managed to encourage onto GNU/Linux.
All are available in the Ubuntu software repos, so installing them is as simple as:
sudo aptitude install ekiga empathy linphone