This is not really an itinerary — unless you have a couple of months and unlimited funds at your disposal — but rather a listing of interesting places scattered around Japan. Find the region you'll be visiting below, and see if you can work in a few of these into your own itinerary. From north to south:
Sado Island — place of exile and gold mines, now featuring the yearly Earth Celebration and the self-proclaimed Alcohol Republic
Eiheiji Temple — head temple of the Soto Zen School of Buddhism. It was founded in 1244 by Zen Master Dogen.
Kiso Valley — Area in southwestern Nagano Prefecture / eastern Gifu Prefecture. Contains a fairly well-preserved section of the old Nakasendo (mountain road used for traveling between Tokyo and Kyoto in olden times) as well as two checkpoint towns, Magome and Tsumago. Going between the two towns makes for a nice hiking day-trip. Onsen abound as well.
Koka — small town near Kyoto famous for its ninja history, unique ceramics and location on the Tokaido Road
Ise Grand Shrine — Recognized as Japan's holiest and most significant shrine, said to enshrine the supreme Shinto deity. The area is also home to the "Wedded Rocks" as well as Toba, the town where pearl cultivation was invented.
Iga — along with Koka, this city is where the art of ninjutsu originated. Every year in April, the town conducts a "Ninja fest" where people can come and dress up in rather authentic ninja garb and wander around town. There is a "ninja house" as well, full of trap doors and other ninja devices.
Yoshino — known throughout Japan as the best place in the nation for cherry blossom viewing, with over 30,000 trees, south of Nara City.
Akiyoshidai — Home to Japan's largest plateau and largest cave.
Takahashi — A beautiful castle town surrounded by mountains, it contains the majestic Bitchu Matsuyama Castle, one of Japan's few remaining original castles, as well as the highest.
Onomichi — A pleasant little temple town home to many Japanese authors. Also the starting point of the Shimanami Kaido, a 70-km journey across the Seto Inland Sea that is considered Japan's best cycling route.
Tsuyama — A beautiful historic town offering Kakuzan Park, one of the best places in the region to view cherry blossoms in the spring, Shurakuen Garden, and Joto Street, a well-preserved historic road located along the pilgrimage route to Izumo Shrine.
Bizen — The city where some of Japan's best swords and pottery originated and continue to be produced today.
Daisen — A city most famous for Mount Daisen, a great place in the West to hike, climb, and skii (in the wintertime). A walk through the trails to Daisen-ji Temple is quite peaceful and serene.
Matsue — Regional hub city with a great atmosphere, two huge lakes, a famous art museum. Nearby Izumo holds Japan's second-most significant Shinto shrine.
Misasa — Home to the mysterious Mitokusan Nageiredo, a temple built into a cliff.