If you use a Windows-style USB keyboard, like Microsoft's Internet Keyboard line, you've probably been aggravated with the Windows key's mapping as the command key -- it's in the wrong place! The simple way to fix this for MS keyboard users is to go to Alessandro Levi Montalcini's Mac OS X page and download his driver for Microsoft USB keyboards. The only thing it does is swap these two keys, but it does it very well :)
Mac OS X Hints
http://hints.macworld.com/article.php?story=20020319103828754