For instance, if Microsoft wanted to learn about technical or trade secrets of competitors communicating through Skype (say, a couple of start-up founders), now they're free to do it.
Is that any different from using, say, Gmail or Google Apps? Not saying that Google is looking at that data but this is a problem with essentially every web-based communication tool. People shouldn't have an expectation of privacy or security just because it's a company they know/like or it's a popular tool.
I've long thought that Google's ability to track searches from Microsoft IP addresses was one of the reasons for the development of Bing - i.e. Bing's value is, in part, that it plugs an information leak and siphons other leaks into Microsoft's data mine.