Does anyone know where are the cheapest connections from (to) Japan?
Do you buy tickets through travel agencies, websites like momondo, or directly from airlines sites?
I would shop around at all the sites mentioned. Flights via third countries are likely to be cheaper than direct flights, although more inconnvenient. Check out flying with Korean Air via Seoul/Inchon, KLM via Amsterdam and Air France via Paris. Try via the airline sites and sites like ebookers.ch
It's worth shopping around because the best deals change often and are not always to be had in the same place.