Tatsuya at FON community inside mixi nicely developed the FON map for Japan (in Japanese) because the official one seems to contain inaccurate information. At the timing of this writing, there are only two access points declared here; yet I am sure a lot of others will join when FON will launch FON-ready router in Japan, which I have been waiting for such a long time.
Take a look at FON community at MIXI コミュを覗ã„ã¦ã¿ã‚‹