I've been using a Mac mini in the office for a few months now and was still struggling with the Windows friendly logitech keyboard I have sitting at my desk. I didn't want to swap out the keyboard because I use it from time to time with my office PC but I was searching for a way to make the keyboard more Mac friendly since I was constantly mis-typing modifier keys. Rather than install additional software on my Mac to re-map the keys and risk system resources and potential conflicts, I found this functionality was already available, but buried in the Mac's System Preferences. I found the answer in System Preferences > Keyboard > Modifier Keys:
If I ever switch keyboards and need to change back, it's a simple as restoring defaults.