Where does MKVToolNix store its settings, its job queue and its cache folder?
First of all only the MKVToolNix GUI stores anytthing in a permanent way. The other programs don't.
Where the GUIs stores its files depends on the operating system and the installation method used.
The settings (the stuff you can configure via its preferences dialog) are stored in a single INI-style file called mkvtoolnix-gui.ini. Deleting this file causes the GUI to revert to its default settings.
The job queue consists of a folder named jobQueue. Inside there's a single file per entry in the job queue. You can move such a file to another installation's jobQueue folder, and it will be picked up automatically. The order of the various files is stored in the mkvtoolnix-gui.ini file mentioned above.
The cache is used for storing file identification results so that adding the same file twice will be sped up greatly. All cache content will be re-created if its missing. Therefore it's safe to delete the whole cache folder.
MKVToolNix GUI stores its settings in a file called mkvtoolnix-gui.ini located in the user's local application data folder. This is usually something like C:\Users\<username>\AppData\Local\bunkus.org\mkvtoolnix-gui. The job queue and the cache are stored in that folder as well in sub-folders called jobQueue and cache.
If you want to restore the settings to their default value you can simply delete the mkvtoolnix-gui.ini file.
Versions prior to 8.3.0 used to store both their settings and their job queue in the registry in the key HKEY_CURRENT_USER\Software\bunkus.org\mkvtoolnix-gui. These settings are migrated to the external and separate files mentioned above automatically when v8.3.0 or later is started for the first time.
Settings are stored in a Windows-style INI file named mkvtoolnix-gui.ini located in the same folder that the GUI's executable file is located in. If you want to reset those settings to their defaults then simply delete the file.
Both MKVToolNix GUI's job queue and its cache are stored in that folder, too, in sub-folders called jobQueue and cache.
Settings are stored a file named $HOME/.config/bunkus.org/mkvtoolnix-gui/mkvtoolnix-gui.ini. The job queue and is stored in that folder as well in sub-folders called jobQueue.
The cache is stored in a different location: $HOME/.cache/bunkus.org/mkvtoolnix-gui.
Settings are stored a file named $HOME/Library/Preferences/bunkus.org/mkvtoolnix-gui/mkvtoolnix-gui.ini. The job queue and is stored in that folder as well in sub-folders called jobQueue.
The cache is stored in a different location: $HOME/Library/Caches/bunkus.org/mkvtoolnix-gui.