By default, My Microsoft Natural Keyboard mapped the Meta key to the Windows button and not to the Alt button. To fix this, run XKeyCaps and load up a keyboard that matches your keyboard. Write down the number on the key you want to be your Meta key (0x40 in my case). Then add the following line to your ~/.xmodmap:
keycode 0x40 = Meta_L
and run: xmodmap -e ‘keycode 0x40 = Meta_L’
Or, just try XKeyCaps for a much friendlier interface to moving keys around.
Now your Alt key should properly generate a Meta event, and your Windows key is free to map to the start menu! 
this .reg is supposed to make caps=ctrl and win=alt but i’ve never tried it:
---------------------------------------- REGEDIT4 [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout] "Scancode Map"=hex:00,00,00,00,00,00,00,00,03,00,00,00,1d,00,3a,00,38,00,5b,e0,00,00,00,00 ----------------------------------------
http://www.gnu.org/software/emacs/windows/faq3.html#capscontrol has more info about this.