Well, they are used to some extent as the Super key in GNOME and KDE (and possibly in other X11 GUI environments). It's used for other functionality, although I've only seen it myself in terms of Compiz effects. I only wish I could take out the Microsoft Windows trademarked logo from those keys...

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Yeah, I've really only seen the "super" key show up as key commands to invoke Compiz effects, so I just reroute those to a combination of Control/Alt/Shift/etc. Having a keyboard with a "super" key labeled with something other than a Windows logo might be nice, but the 101-key layout fits perfectly well for my PC.