JAL is the flag carrier airline of Japan and offers flights from the Americas, Asia and Europe.
Jetstar Australia offers cheap flights to Osaka and Tokyo from Australia.
Once there, the easiest way to get around Japan is undoubtedly on Japan Rail’s vast network of local and interstate trains. Although tickets can be pricey, JR has available to overseas visitors a range of rail passes which allow you unlimited travel on the majority of their lines. Note that JR passes can only be purchased outside of Japan.
For those seeing Japan on a budget, a reputable chain of hostels called J-Hoppers are a good choice of accomodation. They are located in most major cities and offer clean rooms, friendly english speaking staff and are a fun place to meet other travellors and share your stories.
Japan can often be a daunting place for first time visitors unaccustomed to their rigid system of social rules and ettiquettes. Not to fear, the website japan-guide has published online some of the basic everyday rules to get you by.