First of all you should understand which keycode is assigned to which key.
To do this:

# xev

and press the key you want to modify. You'll see something like "keycode XXX".
For example I wan to remap "apple" as "AltGr".
So I give:

# xmodmap -e "keycode 115 = Mode_switch"

that modifies things temporarily and try my setting. If everything works fine, I create in the home directories a .Xmodmap file in which I write:

keycode 115 = Mode_switch

and since I use gdm I create a file named /etc/X11/Xsession.options in which I write:

allow-user-xmodmap

I save and reboot: everything works, mission accomplished.