In Japan, the peak period during summer time is mid August that is called “Obon”. Most of Japanese go back to hometown and stay with family. All transportation will be busy from major cities at the beginning and back to major cities at the end. In 2015, the following dates will be busy.
Outgoing (from major cities) — August 12 and 13. Maybe August 7, 8 and 9 Incoming (to major cities( — August 15 and 16
If you travel during this period, I recommend you to avoid to make a trip to same direction as local tourist. It will be super busy.
And also, the public school is closed from July 20 to August 31 for summer break. This period is busier than usual too.
Fall is very popular season to travel in Japan for local tourist too. JR Group operate lots of seasonal trains during this season and increase the number of trains. I show you seasonal trains information mostly for October and November, 2012 in this post. If you are looking for the information of seasonal train that is operated in September only, please see 2012 summer seasonal trains information.
Fall is good season to travel in Japan. JR Group operate lots of seasonal trains during this season. But it is too many to introduce all seasonal trains. So I pick up the popular trains and are operated in the popular spot.