The FSF suggests that folks use one of the free programs available for Linux and help development by sending in bug reports. They cite China's spying on Skype conversations as a good reason. Does anyone doubt Microsoft is capable of similar? So, even if Microsoft doesn't give Linux (and Mac) users the kibosh, I wouldn't trust them and proprietary software with my phone calls.
Quite an extensive list of alternatives is already compiled at the FSF, some of which I'd never heard of before. But several bring a familiar ring - if you'll pardon the pun.
1. Linphone - Linphone is an internet phone or VoIP much like Skype. It seems the page at the FSF needs a bit of updating, because Linphone 3.4.0 was released in February 2011. The news page states that "the main point of this new release is support for multiple simultaneous calls, with pause, resume and transfer functionality." It is released under the GNU GPL v2 license and commercial support is available as well. It comes in binaries for Debian-based distros or build from source. Here's a screenshot from the Linphone Website: