How to swap command and option modifier keys with a script in OS X Lion
I was able to modify some of the scripts already out there, and get them to work in Lion. To create these scripts:


Run the Applescript Editor
Create two new empty script files (command-N)
Paste in these two scripts
Save them as something like "swap command option" and "restore command option" or whatever you'd like
You can test them by running them in the applescript editor.


Here is the script to swap command to option, and option to command:

#
# Script to swap the Command and Option keys
# in the System Preferences Keyboard settings.
#
# Helpful if using a PC keyboard
#

tell application "System Preferences"
    activate
    set current pane to pane "com.apple.preference.keyboard"
end tell


tell application "System Events"
    tell process "System Preferences"
    click button "Modifier Keys…" of tab group 1 of window "Keyboard"

    # Select keyboard: pop up button
    click pop up button 5 of sheet 1 of window "Keyboard"
    # The 4th choice there.. my USB Keyboard
    click menu item 4 of menu 1 of pop up button 5 of sheet 1 of window "Keyboard"

    # The Option Key pop up
    click pop up button 2 of sheet 1 of window "Keyboard"
    # Change it to Command, the 4th choice
    click menu item 4 of menu 1 of pop up button 2 of sheet 1 of window "Keyboard"

    # The Command Key pop up
    click pop up button 1 of sheet 1 of window "Keyboard"
    # Change it to Option, the 3rd choice
    click menu item 3 of menu 1 of pop up button 1 of sheet 1 of window "Keyboard"

    click button "OK" of sheet 1 of window "Keyboard"

    end tell
end tell

tell application "System Preferences"
    quit
end tell


Here is the script to swap them back:

#
# Script to restore the Command and Option keys to their defaults 
# in the System Preferences Keyboard settings.
#

tell application "System Preferences"
    activate
    set current pane to pane "com.apple.preference.keyboard"
end tell


tell application "System Events"
    tell process "System Preferences"
    click button "Modifier Keys…" of tab group 1 of window "Keyboard"

    # Select keyboard: pop up button
    click pop up button 5 of sheet 1 of window "Keyboard"
    # The 4th choice there.. my USB Keyboard
    click menu item 4 of menu 1 of pop up button 5 of sheet 1 of window "Keyboard"

    # The Option Key pop up
    click pop up button 2 of sheet 1 of window "Keyboard"
    # Change it to Option, the 3rd choice
    click menu item 3 of menu 1 of pop up button 2 of sheet 1 of window "Keyboard"

    # The Command Key pop up
    click pop up button 1 of sheet 1 of window "Keyboard"
    # Change it to Command, the 4th choice
    click menu item 4 of menu 1 of pop up button 1 of sheet 1 of window "Keyboard"

    click button "OK" of sheet 1 of window "Keyboard"

    end tell
end tell

tell application "System Preferences"
    quit
end tell


To make these scripts easy to access, you can go to Applescript Editor Preferences and check "Show Script menu in menu bar". Then, copy your scripts to your home directory Library/Scripts directory, i.e. /Users/ryan/Library/Scripts

Now you can access them right off the menu bar script menu.