If you do have problems with getting Preference settings to stick, where do you look for the property list files containing them?

As a general principle:

• Some sandboxed apps (those with the App Groups entitlement) should now be accessed via ~/Library/Group Containers/[app signature]/Library/Preferences, where [app signature] is something like com.corpname.appname but may be prefaced by alphanumeric characters
• Most sandboxed and non-sandboxed apps should now be accessed via ~/Library/Containers/[app signature]/Data/Library/Preferences, where [app signature] is something like com.corpname.appname
• settings which apply to all users, particularly if they apply before a user logs in, are normally in /Library/Preferences
• settings which apply to an individual user, only after they have logged in, are normally in ~/Library/Preferences (that’s the Library folder in your Home folder)
• settings files should be named something like com.corpname.appname.plist, but many still aren’t.

If you’re in doubt, open the Preferences (or other) folder in which you suspect the file is stored, and order the files by time and date last changed, the newest at the top. Open the app/pane, make a change in the Preferences or other settings, and the property list should shoot to the top of the Finder window.

For some years now, preference files are handled in a deceptive way by macOS. If you try making manual changes to them, those changes are likely to get ignored and reset. Before making any changes to preference files, consult this article for the best solution.

The safest way is to use the command tool defaults in Terminal, with a command such as
defaults delete ~/Library/Preferences/com.appvendor.appname.plist
where com.appvendor.appname.plist is the name of the preference file to be deleted, including the .plist extension. If you use this on preferences stored in the main /Library/Preferences, you’ll need to preface that command with sudo to obtain the necessary elevated privileges. Unfortunately, the defaults tool doesn’t currently work for apps whose preferences are stored in Group Containers.

An excellent GUI preferences editor is Thomas Tempelmann’s free Prefs Editor.

Here is a list of well-known preference files, for macOS Mojave 10.14. These are similar to High Sierra, but earlier versions are more different.

Activity Monitor preferences ~/Library/Preferences/com.apple.ActivityMonitor.plist
Address Book preferences ~/Library/Preferences/com.apple.AddressBook.plist
Airport preferences /Library/Preferences/SystemConfiguration/com.apple.airport.preferences.plist
Ambient light sensor /Library/Preferences/com.apple.iokit.AmbientLightSensor.plist
App preference settings ~/Library/Preferences/[app signature].plist
App Store account settings ~/Library/Preferences/com.apple.appstore.commerce.plist, ~/Library/Preferences/com.apple.commerce.plist and others
App Store autoupdate settings /Library/Preferences/com.apple.commerce.plist
App Store settings ~/Library/Preferences/com.apple.appstore.plist
Apple accounts enabled /Library/Preferences/SystemConfiguration/com.apple.accounts.exists.plist and ~/Library/Preferences/com.apple.accountsd.plist
Apple Remote Desktop /Library/Preferences/com.apple.ARDAgent.plist
Archive Utility ~/Library/Preferences/com.apple.archiveutility.plist
Audio MIDI Setup ~/Library/Preferences/com.apple.audio.AudioMIDISetup.plist
Audio settings /Library/Preferences/Audio/com.apple.audio.DeviceSettings.plist and /Library/Preferences/Audio/com.apple.audio.SystemSettings.plist
Automator ~/Library/Preferences/com.apple.Automator.plist
Bluetooth configuration /Library/Preferences/com.apple.Bluetooth.plist
Calculator exchange rates, etc. ~/Library/Preferences/com.apple.calculateframework.plist
Calendar ~/Library/Preferences/com.apple.iCal.plist
ColorSync calibrations ~/Library/Preferences/com.apple.ColorSyncCalibrator.plist
Contacts ~/Library/Preferences/com.apple.AddressBook.plist
Crash Reporter ~/Library/Preferences/com.apple.CrashReporter.plist (may be defunct)
Date & Time menubar clock ~/Library/Preferences/com.apple.menuextra.clock.plist
Date & Time timezone auto setting /Library/Preferences/com.apple.timezone.auto.plist (may now be defunct)
Dock ~/Library/Preferences/com.apple.dock.plist
Emoji & Symbols palettes ~/Library/Preferences/com.apple.CharacterPaletteIM.plist and ~/Library/Preferences/com.apple.CharacterPicker.plist
Energy Saver settings /Library/Preferences/com.apple.PowerManagement.plist, and in com.apple.PowerManagement.[UUID].plist, where [UUID] is replaced by your hardware UUID.
Find My Mac /Library/Preferences/com.apple.FindMyMac.plist
Finder ~/Library/Preferences/com.apple.finder.plist
Help ~/Library/Preferences/com.apple.help.plist
iBooks ~/Library/Preferences/com.apple.iBooksX.plist
iMessage ~/Library/Preferences/com.apple.imessage.bag.plist
iTunes ~/Library/Preferences/com.apple.iTunes.plist
iTunes, Aperture, iPhoto paths ~/Library/Preferences/com.apple.iApps.plist
Keyboard settings before login /Library/Preferences/com.apple.HIToolbox.plist
Keyboard settings after login ~/Library/Preferences/com.apple.HIToolbox.plist
Login window /Library/Preferences/com.apple.loginwindow.plist
Miscellaneous preferences ~/Library/Preferences/com.apple.systempreferences.plist
Network extensions /Library/Preferences/com.apple.networkextension.plist and /Library/Preferences/com.apple.networkextension.necp.plist
Network interfaces /Library/Preferences/SystemConfiguration/NetworkInterfaces.plist
Network settings /Library/Preferences/SystemConfiguration/preferences.plist
Network Utility ~/Library/Preferences/com.apple.NetworkUtility.plist
Photos ~/Library/Containers/com.apple.Photos/Data/Library/Preferences/com.apple.Photos.plist
Power Management /Library/Preferences/com.apple.PowerManagement.plist, and com.apple.PowerManagement.[UUID].plist, where [UUID] is replaced by your hardware UUID.
Printers /Library/Preferences/org.cups.printers.plist
Remote Access servers /Library/Preferences/SystemConfiguration/com.apple.RemoteAccessServers.plist (may be defunct)
Safari ~/Library/Containers/com.apple.Safari/Data/Library/Preferences/com.apple.Safari.plist
SMB servers /Library/Preferences/SystemConfiguration/com.apple.smb.server.plist (may be defunct)
Software updates /Library/Preferences/com.apple.SoftwareUpdate.plist and ~/Library/Preferences/com.apple.commerce.plist
Spaces ~/Library/Preferences/com.apple.spaces.plist
Spotlight ~/Library/Preferences/com.apple.spotlight.plist
Text substitutions (Keyboard pane, Text tab) in an SQLite database in ~/Library/Dictionaries/CoreDataUbiquitySupport/ under your UUID; not readily editable or removable
Time Machine backups /Library/Preferences/com.apple.TimeMachine.plist
Universal Access ~/Library/Preferences/com.apple.universalaccess.plist
User dictionary in an SQLite database in ~/Library/Dictionaries/CoreDataUbiquitySupport/ under your UUID; not readily editable or removable
WiFi settings /Library/Preferences/SystemConfiguration/com.apple.wifi.message-tracer.plist

Some settings are not stored in preference files. Some essentials are set in the SMC or NVRAM, detailed here. Usernames, passwords, and security certificates are of course stored in keychains, which are covered in several other articles here. Traditional Unix config files are very rarely used by macOS, but may be used by services and servers running on macOS: check their documentation.

Recent Items are kept in ~/Library/Application Support/com.apple.sharedfilelist, and full details are given here. The Launch Services database keeps track of document types and how they relate to apps, and is detailed here. Metadata attached to folders and files is stored in the file system’s volume metadata, and is detailed here.

Thanks to Jeff Johnson @lapcatsoftware for correcting the information about storage of preferences for sandboxed apps above, and for pointing out that defaults doesn’t work with Group Containers.