Changing modifier keys from the command line
Changing preferences and running, defaults -currentHost read -g shows you what changes are being written. I was going to write up a short bash script to automate it, but it looks like I was beaten to the punch:

#!/bin/bash                                                                      

mappingplist=com.apple.keyboard.modifiermapping

if [ $1 == "emacs" ]; then
    echo "Switching to emacs modifiers"
    defaults -currentHost write -g $mappingplist '(                              
                {                                                                
            HIDKeyboardModifierMappingDst = 4;                                   
            HIDKeyboardModifierMappingSrc = 2; },                                
                {                                                                
            HIDKeyboardModifierMappingDst = 12;                                  
            HIDKeyboardModifierMappingSrc = 10;                                  
        },                                                                       
                {                                                                
            HIDKeyboardModifierMappingDst = 2;                                   
            HIDKeyboardModifierMappingSrc = 4;                                   
        },                                                                       
                {                                                                
            HIDKeyboardModifierMappingDst = 10;                                  
            HIDKeyboardModifierMappingSrc = 12;                                  
        })'


else
    echo "Switching to default modifiers"
    defaults -currentHost delete -g $mappingplist
fi



  The script takes one argument, if the
  argument is emacs, then it swaps
  command and control, if the argument
  is anything else it restores the
  defaults.
  
  http://forums.macrumors.com/showthread.php?t=949280