7-Eleven Stores: Seven Bank have announced that starting 11th July 2007, holders of ATM & International cash cards will be able to withdraw Japanese Yen from a Seven Bank ATM. These machines are at 7-Eleven stores in most areas of Japan.
For details, see Seven Bank Ltd.
(Although Visa/Mastercard/American Express are accepted, they state that "some cards bearing these insignias may not be accepted", and there may be a charge (from your bank).

VISA: If you're particularly anxious about knowing where VISA cash machines are, I noticed that they have a website which lists all the locations. Go to the VISA ATM Locator, input the city or town, and it will list all the addresses where ATMs can be found.
You could then even see where each one is on a map: go to Diddlefinger's maps with English labels, choose "English Address Search" and put in the relevant parts of the address. You could even then save the link to that map on the Diddlefinger website, or copy & paste the URL into normal Google Maps.