Most people making flight bookings from Japan to overseas destinations use the big travel agencies such as No1 Travel, HIS, Nihon Ryoku or JTB.
With all the agency fees and add ons, not to mention the time and inconvenience endured to fax or scan travel documents to the agency, it is often quicker and cheaper to make a flight booking direct on the airline's website, especially for flights to the US and the UK (on BA and Virgin).
Check out the deals available on United, Delta and American from such major Japanese airports as Narita, Haneda, Chubu and KIX (Osaka) to the US and you may discover some significant savings on airfares. Other big players for flights to both London and New York are JAL, ANA and Korean Airlines. Air France and Lufthansa fly from Japanese airports to Paris and Frankfurt.
For flights from Europe, America and Australia to Japan most visitors book their tickets online from big online flight comparison sites such as Expedia, saving time and being presented with a choice of airlines.
Flights from Japan to Europe usually leave in the morning, though flights to the USA leave both in the morning and late evening.