Not exactly super
Supercomputers were in the 80's, the 90's saw it become High Performance Computing, the 00's and it became Advanced Computing. One might suggest that this change came roughly with the change from single processor huge vector machines (proper supercomputers, immersed in liquid Freon to keep them cool) to big parallel machines that included massively parallel designs and machines built from commodity processors, but custom everything else (now HPC), and thence to Beowulf clusters, and slowly to machines that are almost totally COTS components (Merley Advanced).
OK, Windows on a a supercomputer.
So where are the apps? It is all well and good to suggest the technically illiterate users will prefer Windows, but high performance applications are a totally different animal to programming for the desktop. Trivial task farming applications will be fine - renderers, sequencing (i.e. BLAST), and the like. After that it gets grim quickly. Software vendors are starting to come to grips with SMP and multi-threaded programming. But distributed memory over MPI is a very different breast. It is hard, and takes a lot of deep knowledge of the possible algorithms, and usually needs tuning to the specifics of the hardware. Speed in MPI systems often requires careful overlap of communication with computation, and this requires knowledge of bandwidth, latency, computation speed, cache effects and so on. Whist there are useful libraries for well understood numeric functions, the idea that you can just link against these and have it all work wonderfully is naive. Any fool can write a parallel version of a program that runs slower than a mono-processor version. Getting even a reasonable fraction of the potential speedup on a distributed system takes real hard slog. We will probably see some of the mechanical CAD apps slowly appear - turnkey FEA, CFD, and the like. But to imagine that any real HPC codes will appear is a different matter.
These little Cray boxes are not supercomputers. Not any more. Supercomputers sit in the Top500. The smallest machine that would have got you into the latest Top 500 has 1500 cores. You will need well over 2000 cores in six months. A noddy little box with a few blades on Infiniband wouldn't get you into the top 10,000. And has been noted above - if MS want to charge a couple of hundred per blade, real supercomputer owners will continue to just say no. The value added by Windows over Linux on a real machine is close to (and mostly less than) zero, most certainly not justifying the hundreds of thousands of dollars MS would want.
Finally, it isn't as if there is anything new in these Cray boxes. They are competing in a very crowded space. About the only slight innovation is the idea that it is a deskside machine and is quiet. They are not the first to try here either. All the others failed. Personally I would not be interested in a machine for compute intensive loads that was not on a proper UPS and was not protected from all the usual reliability issues that plague desktop/deskside machines.