Winginx PHP5 Config
Its name speaks fot itself: the program to configure PHP5 through a window interface. It works directly with the php.ini file, making necessary changes, doesn't break comments nor other settings. So you can edit php.ini both manually (when the program is not running).
Winginx PHP5 Config can work with multiple php.ini files.
Look at the main window:
Through Winginx PHP5 Config you can activate and deactivate PHP extensions, available in the folder ext, Xdebug, Zend Guard Loader and ionCube, too: