Since installing 10.5, I have found that changing the modifier keys (using the Modifier Keys button in the Keyboard tab of the Keyboard & Mouse System Preferences panel) for my USB external keyboard does not work. However, I have found a way to get around this bug...
I changed the modifier keys in the 'All' settings section, and then changed them back in the 'Built-in Keyboard' settings, and this left them modified for only my external keyboard.
Mac OS X Hints
http://hints.macworld.com/article.php?story=200801290442373