I had neglected the CDF player for some time because it seemed to be too limited in its use and especially because I thought it could not be used with third party Applications. However, this appears not to be so and if such is the case then the CDF files have a much greater usefulness than I thought.
If one looks at the structure of the standalone CDF installation there are many of the standard folders of Mathematica. For example, there is an AddOns/Application folder, which can contain third party Applications. I tested this by making a free version of Presentations (available from my web site) and installing it there. There is also a SystemFiles/FrontEnd/StyleSheets folder, which can hold any special style sheets you wish to use with the CDF file. I again tested all this and it worked. A writer of a CDF document, especially if he wished to use extensive code developed in the process of developing the material, could also include his own package.
This does raise the question of whether WRI approves of adding extra files to the Free Wolfram CDF Player and if so what is the best way to do this. It would be nice if a CDF document writer could send an augmented player to his group of readers, but I doubt if this would work.