One thing that I wondered when I heard this new is what will happen to Skype on Linux. Everyone who has used the Skype client on Linux knows that it is not even anywhere near the level of the Windows and Mac client. The Linux client of Skype is plagued with problems of video chat, voice chat etc. And to top it off, there is the lack of updates.
With Microsoft, a company which is anti-Linux, acquiring Skype, it seems like the problems that Linux users face with Skype can only increase. It is unlikely that the Microsoft will discontinue the Linux client of Skype overnight. Microsoft has said in their announcement of Skype's purchase that they will continue to support Skype on non-Microsoft platforms. However, I suspect that the development of the Linux client will come to a complete stop, even though they do not yank out the support for the Linux client. It makes no sense for Microsoft to work on a Linux client for Skype when they can be integrating it with its other products. What this will result in is the Linux client lagging behind further and further until it become obsolete.
Will we see the raise of other VoIP solutions for Linux? Well there is an open source alternative to Skype in development - GNU Free Call. However, from what I heard the project is way to early to be considered a replacement for Skype.
Another view to consider, although unlikely, is that Microsoft might port Skype to .NET. If that happens, it can turn out to be good news for Linux as we could see a Linux client as well under MONO. As mentioned before, this scenario is highly unlikely, though.
Skype on Linux is already bad - really bad. With Microsoft acquiring it, I doubt that the Linux client will ever see an update.