I would like to suggest using PHPRunner41.exe and PHPRunner42.exe, as examples, for different versions of PHPRunner. The reasoning behind this, is for Open With functionality. I had associate .phpr files to open with PHPRunner4.1, which is run by the PHPRunner.exe file. Then, I installed PHPRunner4.2 to test out, and I cannot re-associate PHPRunner4.2 to be the default, even after uninstalling PHPRunner4.1.
This is a Windows "problem". When associating a program to be the default to Open an extension, in the HKEY_CLASSES_ROOT\Application registry path, an key is added, named after the executable (in this case, PHPRunner.exe). Since I already associated PHPRunner.exe with the PHPRunner4.1 executable, windows will not allow me to re-associate the PHPRunner4.2 executable, since a "mapping" with that exe name already exists. I have to go into the registry, remove that entry (or change it by hand to point to the PHPRunner 4.2 executable). Only then, can a new version of PHPRunner be associated with the "Open With" functionality.