I believe autumn is the best season to travel in Japan. Fall color leaves are magnificent. It will be unforgettable moment. JR Group operate lots of seasonal trains during this season and increase the number of trains. I show you seasonal trains information mostly for September, October and November, 2013 in this post.
In Japan, summer school break start from mid July and until end of August. And Obon period in mid August is one of two busiest period in Japan. (Other one is New Years day break) Most of train will be packed. There are so many standing passengers on isle and passenger’s deck.
Ryuhyo Norokko train is operated during very popular Drift Ice season in Hokkaido.
Some part of winter season is the busiest period. Especially in Japan, New Years holidays are crazy busy. In this season, December 28 to 31, January 2, 3 and 6 are expected to be the busiest days. I recommend you to avoid getting a train on those days. The vehicle occupancy rate may be more than 200%. As long as trains have non reserved seat, you can get on anyway without any reservation. But you will be forced to stay on the isle or passenger’s deck without seat. There are many passengers without seats in the train during those busiest days.
As probably you know, it is icy freezing weather in Hokkaido and north part of Honshu island (Tohoku region). If you travel in these cold weather regions, please expect the delay due to snow or high wind. Please have time to spare in your itinerary. Don’t make a tight schedule.
In summer season, the busiest period is mid August. This period is called “Obon (お盆)”. Everybody try to go back to hometown in this period. In this year 2012, August 10 to 19 will be Obon period. Especially the direction to go out from major cities on Aug 10-12 and the direction to go into major cities on Aug 17-19 will be much busier. These dates are weekend days. Everybody will try to move on these dates. If you travel in this period, try to go opposite direction. It makes you to travel much easier.