Here's the smallprint of the customs duty arrangement, but the key point is this:
In 2007, the average applied rate for all goods is 1.8 percent. Specifically, 10.1 percent for agricultural products, 4.6 percent for fish and fish products, and 1.7 percent for wood, pulp, paper and furniture.Also, some things (such as watersports equipment properly labelled as such) don't have to pay fees. A full list of what does and doesn't require payment is available here (current as of 2011). When I say full, I mean it. Everything from ash to spacecraft.
But anyway, if you've bought something small from eBay you won't have much to worry about. Even if you get charged it will be a pretty small amount. I recently spent 150,000 on diving products from America, and was charged 3,200yen on arrival. Not a bad percentage, despite the fact that it should have been free according to the website.