My new keyboard has a convenient switch for disabling the WinKey. It's made for gaming because many games use nearby keys such as LCtrl and spacebar as well as ZXC, and most games react badly to the user accidentally summoning the start menu. It's handy!
Yeah, I've noticed needing something like that with Doom.
I've seen other key-remappers, but sometimes they're really poor with modifier keys like Ctrl and what not, (sometimes useful for funky Laptops) which might tie into something fundamental about the legacy of keyboard hardware, but it's still annoying.
My favorite keyboard are the IBM 102 key bucking spring battleships. No Windows keys on them.