Windows – How to disable or reassign the ‘Windows’ key

You can use an application like ControllerMate to assign custom actions/scripts to keys and controllers.

Non XFCE-related stuff

It won't be exactly an answer to your problem, sorry for that, but still should be useful for someone at least. In Gnome it was fixed in recent Ubuntus. By it I mean treating Win not as a modifier key. In the old days, e.g. in Ubuntu 9.04, you had to do following change:

Go to System -> Preferences -> Keyboard, under Layouts tab click Layout options... button and in Alt/Win key behavior list choose Meta is mapped to Win keys (or Meta is mapped to Left Win) instead of Default.

What it really does? Changes altwin option in $HOME/.gconf/desktop/gnome/peripherals/keyboard/kbd/%gconf.xml file (or creates it if it does not exist):

<?xml version="1.0"?>
<gconf>
        <entry name="options" mtime="1298496603" type="list" ltype="string">
                <li type="string">
                        <stringvalue>altwin     altwin:meta_win</stringvalue>
                </li>
        </entry>
</gconf>

If you've chosen Left Win, then there will be following string value:

altwin     altwin:left_meta_win

In Ubuntu 10.10 it's not needed as Default apparently has changed.

But you have XFCE, not Gnome, so this rather won't help you.

XFCE-related stuff

I've downloaded Xubuntu (9.10), played with it a bit and finally found a solution.

Firstly, though, I must say that keyboard settings are really screwed in XFCE. In Settings -> Keyboard under Layout tab you don't have too many options. You cannot change XkbOptions there and even if you do it manually in ~/.config/xfce4/xfconf/xfce-perchannel-xml/keyboard-layout.xml, it will be overwritten. So I've changed /etc/default/console-setup by adding altwin:meta_win to XKBOPTIONS (use comma as separator if there are some other option(s) already). Still, no luck.

tl;dr

What's the solution?

Do not care about XFCE way of handling keyboard, because it's apparently broken. Use setxkbmap directly:

setxkbmap -option altwin:meta_win

(or left_meta_win, whatever you prefer)

Now you have to check that it really solved your problem. :)

How to apply it permanently?

echo -option altwin:meta_win >>~/.Xkbmap

It can be also done for all users by writing to /etc/X11/Xkbmap instead.

How can I quickly check if altwin:meta_win or altwin:left_meta_win has been applied?

setxkbmap -print

Line with xkb_symbols should have something like altwin(meta_win).