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)
There are unfortunately very few websites of Japan-based travel agencies in English. If you read Japanese, try Yahoo Japan Travel, which has one of the largest selection and easy to use, highly customizable search engine, and STA Travel, which has discounted flights and packages inside Japan.