Pricenoia lets you compare prices for the same book on all of Amazon's sites (.com, .co.jp, .co.uk etc.) including shipping costs! I added the quick compare bookmarklet to Firefox, browsed to the page for a book I had recently bought and tested it out. The Amazon Japan site uses the non-discounted US$ price to make the books look cheaper. Although I was aware of this I'd never bothered to do a comparison of the discounted US price with the yen price so was surprised to see that the discounted price on the US site was quite a bit cheaper. Unfortunately the 1,300 yen shipping costs from Amazon.com negated the saving, but I'll be sure to run this check before purchasing future books, just in case. They also have a mobile site.
(Being a skeptic I also went the the amazon.com site and double checked that the shipping prices that Pricenoia had provided where correct. They were and where conveniently converted into yen)