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.
