Dmatigs answer should already work. I just want to add that if you are having trouble finding the keycode you can either look into the keymap you are using in /usr/share/rdesktop/, or alternatively you should be able to use the keysym (the name X11 uses for that key, for example Super_L for left Windows key) instead of the keycode.
And you probably have to do something like xmodmap -e 'clear mod4' if you want to modify Super_L (since it is what X11 calls an 'modifier' key), and then add Super_R back again with xmodmap -e 'add mod4 = Super_R'.
xmodmap -e 'clear mod4'
xmodmap -e 'add mod4 = Super_R'
xmodmap -e 'keysym Super_L = less greater'
That's how I would try to do it. The two keysyms behind the equal in the last line are for normal key presses and shift+key respectivly. You can add up to 6 (possibly even more, but I am not sure) of these for all kinds of different modifier groups (alt, ctrl, ISO_Level3_Shift aka alt gr).
Lastly, place the commands (only the parts behind the -e, not the whole xmodmap call) in a file called .Xmodmap in your home directory, that will make X11 load up your configuration every time you start your desktop session.