Yeah, in science, it's usually rare to have serious development done on Windows, except for the occasional data acquisition station or for some control computer attached to a commercial lab apparatus. Just have a look at the Top 500 supercomputer clusters, most of them run a flavor of Linux or UNIX. I've worked for genomics companies and now I'm at a neurological institute, and all the heavy duty HPC pipelines are designed to integrate with such clusters, and the scientists themselves work on Linux desktops. We're shuffling terabytes of medical images back and forth, with large data trees on shared filesystems that are continuously updated by scripts in bash, Perl, Ruby, Python, and Java. If Microsoft had the power to force us to switch to Windows for everything, science would grind to a halt for 15 years while we re-code everything, and even then it would probably still not be as functional as what we have right now. There is great beauty and power in command-line processing, when done well.
Does anyone know of any big science project that's all done on Windows? Really, I'm asking because I'm curious. As far as I know, in physics, chemistry, astronomy, geology, medecine etc, any project that requires complex custom HPC pipelines are created on Linux (or UNIX). Windows? Never heard of one. But it might exist, I suppose.