Have you ever researched the cost of a fountain drink to a business? In some places, it costs mere pennies for enough syrup to make a few hundred glasses of Coke. While I'm sure that this is slightly more expensive in Japan (as many things are), it's not greatly more expensive, yet free refills are almost unheard of in most parts. Costco Japan's food court is a rare exception to the rule. I'm actually not too terribly fussed about the lack of free refills as I'm not really the type of person who needs to down a liter of soda with a meal. However, I am annoyed at a different sort of petty stinginess in Japan and that's the partially filled glass. What is worse, if you ask for a drink without ice, you will get a proportionally reduced amount of liquid in your glass. If it is 80% full with ice, you'll get it 60% full without ice.
This sort of pettiness flies in the face of the idea of "good customer service" (which goes beyond a bow and polite words, much as many think that's all it is about), and I won't miss it.