Just a warning about using ATMs in Japan - I generally use ATMs wherever I go.
I found that a pretty small proportion of ATMs accepted Cirrus or Plus - certainly most Japanese bank ATMs didn't. As pointed out above, Citibank ATMs were OK, but are pretty much just in the main cities.
However the thing that really helped me out in the end is that Japan Post Office ATMs now accept VISA/Plus cards, and they are pretty much everywhere.