Open source only seems to win in domains in which it makes sense for companies to share work in order to compete at a higher tier of functionality.
The only way it realistically can realistically happen if is the commercial product is not being improved (i.e. differentiated) any more. Your example is one of these - standardization is related to commodification.
I suspect also that user-facing apps are easier to keep improving, because the user is right there, and always has more needs that could be served (e.g. text editors will evolve til they can read mail; those that can't will be replaced by those that can). Non-user facing apps tend to be defined by their environment, rather than by users - although, any component that creates a benefit that the user wants more of will keep being improved (from Clayton Christensen). e.g. databases, CPUs.
I don't think it makes sense to make generalizations about where "open source seems to win". Things are changing too fast; the circumstances that made it possible for Mozilla to beat IE in the mid-2000s no longer exist, for example.
But I agree with you and think that in the long run, open source is a big winner in infrastructure software, and generally just that.
R's integration with free data sets is crazy. For quick analysis it is great. For development Numpy/SciPy/Matplotlib/PyCUDA is more suitable.