Apple has built a similar feature into the System Preferences. Open the System Preferences application and click 'Keyboard & Mouse'. Then click the 'Modifier Keys…' button in the bottom left. Re-map your keys and click OK. I change mine to look like this picture:
Unfortunately, OS X applies these changes to all keyboards — so if you have a PowerBook or iBook with a PC keyboard plugged in, you'll have to re-map the modifier keys whenever you want to use your laptop's keyboard. If I recall correctly, uControl applies your changes to the keyboard you specify, so it swaps back and forth automatically. Sometimes progress isn't always in the right direction…