If you are backing up your home folder, you are also backing up your user prefs all of which are stored in "Your User Name"/Library/Preferences. There are several other "Preferences" folders that contain "global" prefs, namely /Library/Preferences and /System/Library/Preferences.
One potential "trap" though... corrupted prefs files are often the cause of anomalous system behavour so saved prefs should be copied back into new folders with caution.
