Add the following to your ~/.Xmodmap file:
clear control clear mod4
keycode 105 = keycode 206 =
keycode 133 = Control_L NoSymbol Control_L keycode 134 = Control_R NoSymbol Control_R keycode 37 = Super_L NoSymbol Super_L
add control = Control_L add control = Control_R add mod4 = Super_L To test this right now, just do xmodmap ~/.Xmodmap
Now, to have this happen every time at startup, add to the end of your (and/or create a new) ~/.xinitrc file the following:
xmodmap ~/.Xmodmap