I don't think joblessjunkie is criticizing the command key (I personally don't mind either the Windows or Mac placement).

He's saying that the ctrl and the fn key (used to access the function keys instead of brightness/expose/volume/etc) should be swapped. I completely agree; I never use the fn key and my pinkie ends up bending for the control key.

I used Keymap4Macbook for a while, but found it easier to do the remapping in Emacs (with (setq mac-function-modifier 'control)) and use Emacs's eshell mode rather than a terminal emulator to run interactive shells. The only time I use the control key outside of Emacs and interactive shells is to control-click when I cannot right-click (because, e.g., I am using the Macbook's internal trackpad) and in that situation I found it simple enough to train my muscle memory to hit the second-to-leftmost modifier key rather than the rightmost modifier key. In contrast, retraining my muscles to use anything but the rightmost modifier key to "set the control bit" in Emacs would have taken a lot of time and attention.

(On OS X, control-click does the same thing as right-click, namely pop up a contextual menu, and you can only right-click if you have a non-Apple pointing device.)