Here's what I do:
Create a file called .Xmodmap in your home dir. It contains:
[code:1]
keycode 115=F13
keycode 116=F14
keycode 117=F15
[/code:1]
This binds Win-L to F13, Win-R to F14 and that context menu type button to F15. To get X to see this run
[code:1]
~$ xmodmap .Xmodmap
[/code:1]
I put a script in KDE's Autostart dir to run this every time KDE starts up. It's a little, hacky, but it works. There's probably a way to have X do this rather than KDE.
The disadvantage is that you lose the ability to use the extra keys as modifiers. Because of this I only bind the Win-R key (116 = F14) and leave the other two unbound (or they can be set to Super_L and Menu, respectively, which is the same thing).