Although there are plenty of flights from Europe to Japan but if your nearest international airport does not have direct flights to Japan, may be a flight via Middle east is an option to choose.
Especially Emirates and Qatar Airways have various flights to Europe from Dubai or Doha airports. These two airlines are widely known as excellent services and their hub airports offer wide range of duty free items during your transit. Also these airlines' offers are cheaper than European airlines.
On the other hand, negative thing of Middle east airlines are that flight duration is much longer than transit in Europe. Therefore you have to choose either cheaper air ticket or shorter flight duration.