Support for special Natural Ergonomic Keyboard 4000 hotkeys on OS X 10.11
You can use ControllerMate by Ordered Bytes (costs $25) to regain control over the special keys of the Natural Ergonomic 4000. It should recognise all keys, even the shortcut keys.

Note: To get the "My Favourites" keys working, download the profile at: http://www.orderedbytes.com/controllermate/compatibility/#microsoft/ergonomic_keyboard_4000