Be warned that summer in Tokyo is really hot. The bright side is that almost any cafe, restaurant, etc. is air-conditioned. Expecially during the summer, most cafes and restaurants would give you a glass of cold water with ice cubes on arrival for free even before you order anything, and you can ask for free refills.
OBON
For a few days around August 15th (about August 11th to 16th this year), many people take holidays and travel home to join their family. At the beginning of Obon, trains and all transports from Tokyo to other areas will be very busy. At the end of Obom, transports toward Tokyo will be busy. Reserved seats for Shinkansen (bullet train) gets easily sold out, and cars with non-reserved seats may become like a subway during rush-hours, so it is a good idea to avoid traveling to or from big cities in this period. Plan wisely and book ahead if necessary. On the other hand, public transport within Tokyo will be less crowded than usual during this period. But if you really need to travel between big cities like, for example, Osaka to Tokyo, local trains might be an option on some routes, so ask locals. Highways will also be crowded and there will be long queues, so if you are taking long-distance buses, expect big delays on some routes. Again, if you are a traveler, it is probably best not to move between big cities during this season. And traveling inside Tokyo will be much more comfortable than usual, because there will be much less commuters.
NEW YEAR
Most people don't work between January 1st and 3rd. While many people stay home with family, some travel abroad.
SAKURA
Depends on regions of Japan. Late March - Early April.
SCHOOL YEAR
School year starts in April, as well as fiscal year.
GOLDEN WEEK
Several national holidays are concentrated between the end of April and early May, and it is called the Golden Week. As you can expect, many people go on vacation, and touristic spots get very crowded. On the other hand, parts of central Tokyo may be less crowded because there wil be less commuters.
SUMMER VACATION
School vacation starts around July 20 and lasts till the end of August. Many workers take their holidays between July and September. Many people take holidays during "OBON", a special period in August, during which even Shinkansen bullet trains get extremely difficult to book. Touristic spots also get very crowded.
CHRISTMAS
Christmas is not a national holiday in Japan. Although destinations for young couple may get crowded or fully booked, life goes almost just as in normal times.
