Where does Mountain Lion's Calendar.app store its preferences?
The bundle identifier is still com.apple.iCal. You can see it from the Info.plist or with something like bid() { osascript -e "id of app \"$*\""; }.

So the property list for the preferences is still in ~/Library/Preferences/com.apple.iCal.plist. It will be probably be moved to ~/Library/Containers/com.apple.iCal/Data/Library/Preferences/com.apple.iCal.plist if Apple sandboxes Calendar.