I eventually managed to get it to work from the official Emacs 25.1
release, so I think that the problem has been fixed.
This is the form I used:
(when (eq system-type 'windows-nt)
(setq w32-pass-lwindow-to-system nil)
(setq w32-pass-apps-to-system nil)
(setq w32-lwindow-modifier 'super)
;; My laptop does not have a right super, so I used the
;; 'apps'/'menu' key instead.
(setq w32-apps-modifier 'hyper))
Also note that even still, Windows still ate a lot of the attempted
super key combos, even those that didn't look like they did anything
(s-z, for example). I know that `s-w` was passed to Emacs, as well as
most of the symbol characters ('[', ';', etc...).
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