To figure out if Emacs is recognizing your Alt key at all: type C-h c
, then some key combination that starts with Alt, e.g. Alt-f.
If it says "M-f runs the command forward-word
" (for example), then Emacs thinks of your Alt key as a Meta key too, and anything you bind to Meta will work with both the Windows key and the Alt key, so there is no way to make the Alt key work differently from the Windows key.
If it says "Hyper f is undefined
" or "Super f is undefined
" (for example) then Emacs recognizes your Alt key as either Hyper or Super respectively, and you can bind commands to keybindings starting with Hyper or Super, and those will work with your Alt key.
If it doesn't react at all, then it means it's not recognizing the Alt key as anything, and there is nothing you can do from within Emacs: Emacs doesn't even get the key. In this case, as the other answer said, you should look up the equivalent of xmodmap
for Windows -- it's something to do with the registry; the GNU Emacs FAQ for Windows's section on How do I swap CapsLock and Control? has some relevant details about this ("Scancode); also see this page.