Virtual Microscope is an excellent, free (gpl) Windows software part of this new science and technology software category. It is a software product made by Sandia Corporation, which claims to offer high resolution and high image quality image of electron microscope. I was not able to test it at my time but from what I have read and heard about it, the software is indeed the real deal and could be considered the best free software for electron microscope. It is available for free download in its trial version, so one could try it first before purchasing it.
However, there are limitations of Virtual Microscope as a free product, as it does not come with any of those software applications that come with your computer such as Windows application or Word. You will also be limited in the program options as it only comes with a fixed number of software programs and cannot be modified. But for basic education software and basic microscopy research, then I believe it is worth for testing and trying.
In the meantime, you can search for and download other free software for virtual microscope from net. To me, it seems like the better option to go with, considering how much the price is on the trial version, and the fact that it comes with the whole set of programs. At the moment, NLS and JML are two of the most popular ones, along with Virtual Microscopes. With a little bit of research, you will surely find the right software for you.