I have a Windows keyboard (MS natural 4K), I'm using Mac OS X, and I like to use Emacs. However, the default Mac OS X GUI build for Emacs has the Windows key mapped to Meta (meta typically is the Alt key). This is not very comfortable, and I would like to remap it. Note that in the rest of my environment, Alt is really alt, and the Windows key typically shows up as the Apple key.
(setq mac-command-modifier 'alt) ;; Can be set to meta, alt, super, or hyper
I'm not sure how your windows keys map, but you can evaluate that expression in a scratch buffer with C-x C-e until you find modifier you like and then copy it to your init.el or .emacs file.
Installing Emacs 23 solved this problem. Thank you, Richard Hoskins, for giving me the push to get Emacs 23.