I'm planning to be in Japan from 15/05/08 - 03/06/08. I believe I'll be arriving one week after Golden Week which finishes on the 5th May. Ideally how early should I be booking accommodation directly with the Hotels throughout Japan?
I would normally booking international flights & accommodation approx. 6 months before - but I'm worried that mightn't be enough?


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<hr>I would normally booking international flights & accommodation approx. 6 months before <hr></blockquote>
this is a wind up right?

I would say yes to be safe. Some people vacation time runs over a bit. You might not have any problems but you should spend your trip worrying about where to eat/what to see and not where to sleep.
Many hotels in Japan, esp at the lower end of the price scale, don't take bookings more than 2-3 months in advance (e.g. Toyoko Inn). After the Golden Week, it shouldn't normally be a problem finding somewhere to stay, though look out for some local festivals, esp over a weekend when the whole town often sells out.
After the New Year seems early enough for you to start contacting hotels.

I visited japan from 20th May - 9th June this year.
We booked first 2 nights hotels and nothing else, we just went online/called hotels night before arriving in city and booked then. We got every hotel/ryokan we wanted and had absolutely no problems. Booking everything 6 months in advance means you are locked in to an iteniary and you don't have freedom so stay longer if you like somewhere or move on sooner if you don't.

If you are arriving on May 15, then the Golden Week crowd will have gone away, and there will be a lot of empty rooms. You are arriving at an excellent time! Good weather, crowd gone, rooms open. You really need not book ahead much for your timing. As #5 says, you can just about get anything you want upon arrival. You are in for a good travel in Japan!