Howdy!
I've been at this for a while, and until now without success. It seemed impossible to map the fn key if it wasn't recognized by your computer since it doesn't send out a scan code you can use to remap it.
Then I found a DLL file on this forum written by Micha:
DLLCall: Support for Human Interface devices. With this DLL it's possible to get a response back for a number of special keys, also Fn keys. So based on this DLL I wrote a script that checks whether the Fn key is pressed or released, so it can function as a modifier and you can use it in any way you'd like.
Since the matter of remapping the Fn key has been a problem for so many people for quite a while now, I created a complete guide explaining every step in full detail. The guide, and all the relevant files and information that comes along with it, can be found at:
http://brrp.mine.nu/fnkey/
http://yotz.eu/fnkey/
All this is based on the remapping of my Apple Wireless Keyboard, now with full use of the Fn key as a modifier and also the Eject key. From what I gather, the DLL has helped a lot of people already to remap single action keys and in doing so has proven its worth. That's why I'm confident that this method for remapping the Fn key will work on a wide variety of keyboards.
I hope this solves the Fn key mapping problem for all the people who've been looking for a solution all this time. Feedback on the script and on whether you succeeded is much appreciated.
Good luck!