I think open-source eventually replaces commercial products, in the same way that proprietary products become commoditized. The response for commercial products is also the same: continual differentiation, adding new features, benefits, support, documentation etc. Exceptions are also the same: natural monopolies (e.g. strong network effects). Open-source is great at hill-climbing, where there are clear directions for…
Counter-examples abound. Can you name even one open source app that has displaced a mature, user-facing desktop app with a non-trivial UI, other than a web browser? 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.
R's integration with free data sets is crazy. For quick analysis it is great. For development Numpy/SciPy/Matplotlib/PyCUDA is more suitable.