The shortcuts that can be set in System Preferences > Keyboard > Keyboard Shortcuts > Application Shortcuts are stored in `~/Library/Preferences/.GlobalPreferences.plist` and the property lists of applications (like `~/Library/Preferences/com.apple.iTunes.plist` or `~/Library/Containers/com.apple.chess/Data/Library/Preferences/com.apple.chess.plist`).

The shortcuts for services are stored in [~/Library/Preferences/pbs.plist](http://apple.stackexchange.com/questions/79626/set-keystroke-for-service-from-terminal/79663#79663).