Normally you control a computer with a keyboard and mouse. But, the the purpose of a Raspberry Pi is to invent something new. To that end, you have have to come up with some new, creative ways to get information into the RPi. The Wii controllers are a miracle of engineering and communicate to the Wii (and whatever else you would like) using Bluetooth. Using a USB Bluetooth interface and some simple programming you can use the Wii controller as an input for whatever you need. Check out this video:
If you need more information on the subject, see the Brian’s Life Blog. Also, I will be posting a follow-up on how to connect the balance board.