Just guessing here but I think it's to allow easy grounding of old appliances and other equipment that might risk contact with electricity but are not grounded by default. Metal frame desk as example.

And the cable on the left here is what the included Apple MacBook power cable looks like, with the little earth wire sticking out to screw on http://rinare.com/wp-content/uploads/image_archive/110801_2....

I think it's just a legacy thing - historically, the only things that needed grounding were static appliances like fridges, washing machines and air conditioners. The manual in our fridge has this instruction for earthing http://mayoyo.tokyo/jIe.jpg

I need to revise my comment that "I don't think I've ever seen a three-prong outlet in Japan", because now that I have power sockets on my mind, I just saw a three-prong outlet at my gym. So I guess newer buildings have them.