On my Apple Powerbook running Ubuntu natively.
pyara 9 [~] % cat .xmodmaprc
pointer = 1 3 2
keycode 37 = Control_L
keycode 64 = Control_L
keycode 105 = Super_R
keycode 108 = Control_R
keycode 133 = Alt_L
keycode 134 = Alt_R
clear control
clear mod1
clear mod4
add control = Control_L
add control = Control_R
add mod1 = Alt_L
add mod1 = Alt_R