I have bound left-window to Super, right-window to Compose, and menu to Hyper. XEmacs has been configured to lots of Hyper-key combinations; my window manager (fvwm2) uses Super-key combinations almost exclusively. Thus the window manager is more or less completely controllable from the keyboard, without interfering with programs that want meta keypresses. And, of course, you can never have too many keybindings in Emacs.
For reference, here are the relevant bits of my .Xmodmap:
add mod2 = Super_L
add mod3 = Hyper_R
Depending on your keyboard and your X settings, you may need to specify key codes other than 115, 116, and 117. To determine what key code X is generating for these keys, run
xev and press the key. You should get something like:
KeyRelease event, serial 19, synthetic NO, window 0x6400001,
root 0x26, subw 0x0, time 597817457, (-204,666), root:(849,689),
state 0x0, keycode 115 (keysym 0x0, NoSymbol), same_screen YES,
XLookupString gives 1 characters: ""
The number following keycode is what you need to use.
Also, you may need to make Super
mod4 instead, depending on whether you have num lock mapped to mod2. Me? I have my num lock key mapped to something else entirely.