If you look a little bit around in the extremly confusing extensions area of magento connect, there are already some more payment plugins posted although Magento 1.0 is out only for a months or so..

I guess you just have to wait some more and suggest some good Japanese gateways which should be included.

For Japan and Magento, you are right.  There isn’t much in the way of payment/shipping.  What I will be setting up, is PayPal, C.O.D. and Bank transfer, for the basics.

I would say C.O.D. is the most used, even if you put a charge on the shipping/payment method of C.O.D., Japanese will pick this because it is safe.

After this, I would say Bank transfer, and then credit card.

The good thing about PayPal, is it can take Japanese characters no problem.  I have used some other payment methods in the past, but I find PayPal is the most cost effected. 

I really hope to see PayPals Website Payments Pro Solution for Japan.  That would be a great option.

You are going to need to do some custom code, or alter some payment modules that already exist to get what you need.

I am surprised that bank transfer and C.O.D. did not come stock with Magneto as it would be simple to do.  If no one gets around to making them, then I am sure I will do it when the time comes for me to use them.  Until then, I just don’t have the time as I have to address my clients needs first.

Regards,
CKD

another interesting thing might be econtext which has conbini support and an alliance with partners in china and korea (--> payments in these countries can be made over this gateway too)
There are also some links to running webshops posted.

http://www.econtext.co.jp/home.html