Solution: place the following lines inside the file .Xmodmap in your user's folder (at the top level):
! ~/.Xmodmap
clear Mod2
clear control
keycode 63 = Control_L
keycode 67 = Control_L
add control = Control_L
This will change the keyboard mapping under X11, such that the Command key acts like the Control key, so you will be able to use either the Command key or the Control key within X11 apps for shortcuts. More details can be found in this article.
[robg adds: We've run a number of other hints on modifying .Xmodmap for various purposes.]

