Travelling abroad from Japan can be both cheaper and much more expensive than coming to Japan from another country.
The reason is that flights from Japan have highly seasonal prices. The following periods should be avoided, as these are Japanese national holidays and prices can triple or quadruple :
New Year (27/12 to 3/1), Golden Week (29/4 to 5/5), from late July to the end of August (especially "Obon", mid-August).
If you read Japanese, you might also consider checking Yahoo Japan Travel, which has one of the largest selection and easy to use, highly customizable search engine, and Tocoo, which has discounted flights and packages inside Japan.
