All CCleaner INI files must be located in the application installation folder (typically, C:\Program Files\CCleaner). By default, none of the INI files exist when you first install the application.
Winapp2.ini - If you create this INI file, you can add entries for new software that CCleaner can clean. See How to add your own program for CCleaner to clean.
Winapp1.ini - If you create this INI file, any applications you list in it will replace the default applications on the Applications tab of the Cleaner area. See the same section for more information.
Winsys2.ini - If you create this INI file, you can add new areas of Windows files or Registry items for CCleaner to clean. See How to add other areas of Windows for CCleaner to clean.
Winsys1.ini - If you create this INI file, any areas of Windows you list in it will replace the default ones on the Windows tab of the Cleaner area. See the same section for more information.
CCleaner.ini - This file contains all settings for CCleaner that can be set within the program. If you are running CCleaner Portable, or if you set CCleaner to save its settings to an INI file (see Changing Advanced Settings, CCleaner will save its settings to CCleaner.ini. For more information on modifying this INI file, see Using CCleaner.ini to modify how CCleaner runs.
Note: The portable version of CCleaner 'knows' that it is portable because of the presence of the file portable.dat in the application folder. If CCleaner finds the file portable.dat in the application folder, it will always save its settings to CCleaner.ini. The contents of the portable.dat file do not matter - you can create a dummy file.