According to Wikipedia, Skype was thinking of making its traffic available to the NSA before the acquisition.
So, I am making two points right now:
1. All large IT companies are approached at some point by governments all over the world. So it is not Microsoft which is specifically evil, it is the way the society is structured now. I see no reason to single out Microsoft as a problem. You don't know what GitHub is doing now either.
2. As a separate point - large businesses are not "evil". They are comprised of normal people who want to do good. I know many people who work in Microsoft, Apple and Google, including some pretty high in management. None of them are evil. And I doubt the founders of these companies are evil too. The behavior of these companies is explained by an interaction of their business success and the current structure of society. In authoritarian societies this is much worse news than in the democratic societies.
The reason I bring these points up is because I feel that Microsoft is singled out unfairly. It is not a bad company and it has a lot of pretty good products, and its behavior is not governed by evil intent, but rather by a complex interaction of business incentives, government regulation and corporate structure that is necessary to manage a large company. That does not mean this mix of incentives does not create negative results - it does sometimes - but I feel that in the FLOSS community many see it as almost a conspiracy by someone in Microsoft to destroy the world. Which is just untrue.
Louigi.