Apple apps - inconsistent. Some basic settings in prefs, sometimes settings in System Prefs.
Apple utilities - a few settings in the window buttons or menus, but many prefs you would like to have aren't anywhere. The GUI has been simplified, to keep simple-minded people happy. I don't know anyone else who is happy with removal of advanced settings.
3rd party apps - usually have a healthy prefs menu.
3rd party services / daemons - may have a custom System Pref pane. Also may use a config text file, especially if they were ported from the *nix world.
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