I lived in Hikone, Shiga-ken for four months, studying abroad, and I've been in Yokohama for five years. I've traveled a fair bit - Hokkaido, Okinawa (Ishigaki and Iriomote only), Kansai area (Kyoto, Nara, Kobe, Himeji), and around Tokyo (Hakone, Kamakura, Izu Peninsula, and up to Nikko).
Unfortunately only holidayed in Japan... I'm hoping one day to live and work out there for a bit, but at the moment prospects of that happening are pretty grim.
When I've been out there I've done Tokyo, Osaka, Kyoto, Nara, Himeji, Kobe, Hiroshima, and Nikko. Hoping to head a bit further and either go for Hokkaido or Okinawa next time (and some of the bigger cities along the way)