Funny I was putting together the same project around the same time. I just finished it late last week and have used it a couple of times. I have an Adafruit data logger shield and just save the nunchuck data every 200ms, which results in about 5Mb of data through the night. Then I remove the SD card from the shield in the morning and load it into Excel and do my data manipulation and plotting there. If you need to run the analysis live on the Arduino, the root of the squares that AWOL suggested sounds fine.
It works pretty well, although last night my son ripped out the wires from the breadboard while he was thrashing around in the middle of the night. I'd love to figure out how to get my wireless nunchucks to work as that would solve that problem. I was also hoping to collect some microphone (sound level) data concurrently, but that is also proving to be more complicated than I had anticipated.