Xah Lee, 2007-12, 2011-06
This page gives some tips on how to swap the Command key with Option key on Mac OS X. (or switching any modifier keys)
Starting with Mac OS X version 10.4, you can switch modifier keys to any other. This is done in “System Preferences”, “Keyboard & Mouse”.
For more advanced key swapping, see: Mac OS X Keyboard Layout, Keymapping, Keybinding, Tools.
For Windows, you can use AutoHotkey, you can use my software: How to Swap Caps Lock, Alt, Control Keys on Windows.
For general tools, see: Keyboard Layout & Key Macro tools for Windows.