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Depends on which universities you are talking about. Here in the US, Microsoft has their hands in the pants of most schools and they try to get programs built around their software because they are in the industry standard in this country. There's no getting around that. Many of those schools do have Linux classes though or at the very least, LUGs around the area, but Microsoft software is the name of the game for the most part.
There are certain subjects that are simply never going to use Windows. For example, any course dealing with high-performance or large-scale computing just isn't going to happen on Windows. Others are harder to do on windows. For example, my C/C++ course used windows machines, but the only thing we used them for is SSHing into a Linux server where all the actual work happened. (these were two different universities, btw). A python or perl course would likely be handled similarly.