Fisco
It is not one of the major Japanese cryptocurrency exchanges (BitFlyer, QUOINE, Zaif), but nonetheless it was granted a license by the Japanese Financial Services Agency (JFSA).
The biggest advantage of Fisco exchange is the fact that it holds a license by JFSA, as required by local law. Japan has one of the most developed bitcoin communities, while the majority of the exchanges worldwide still operate in the gray area.
Clients if this exchange are only charged with withdrawal fees. Taking into account that the majority of exchanges charge 0.15% - 0.25% per trade, and many of them also apply fees to deposits, this makes Fisco really stand out.
The web-based platform provided by Fisco is nothing special in the crypto world, yet it is nicely designed and seems equipped with all the basic tools.