System settings that aren’t in System Settings
It's now a habit to save all my changes in system and app preferences in a script.First I do a    defaults read > 1

Then I change the setting in the app or System Settings, then back on the commandline, I do    defaults read > 2
    diff 1 2

The change gets copied to a preferences.sh file with a whole bunch of statements like:    defaults write com.apple.ical "Show Week Numbers" -bool true

Afterwards, I don't care where the setting is. I just set it in my preferences.sh file, and if I update any of it, I run that file.