This is something of a whirlwind trip, but it allows you to take in some of the best that Honshu has to offer. If you have 1 or 2 extra days, you might wish to devote more time to Kyoto or head over to Kyushu.
Day 1: Arrive in Tokyo
After your arrival at Narita Airport, head to your Tokyo hotel (about a 2-hr. trip). Recuperate from your flight, settle in, and get a feel for the city, take a walk through a nearby neighborhood and top off the day with a meal in a traditional restaurant. Stay up as late as you can to adjust to the new time zone.
Day 2: Exploring Tokyo
Because of the difference in time zones, you'll probably be wide awake in the wee hours of the morning, so get up and head for Tsukiji Fish Market. After a breakfast of fresh sushi, head to Hama Rikyu, one of Tokyo's oldest Japanese gardens (open at 9am), from which you can board a ferry for a cruise up the Sumida River to Asakusa, where you can visit Sensoji Temple and shop for souvenirs along Nakamise Dori. Afterward, see the Tokyo National Museum, the world's finest repository of Japanese art and crafts. Toward evening, head to Ginza for a stroll through a department store, and then try to attend a kabuki play.
Day 3: More of Tokyo
Visit the Edo-Tokyo Museum for a colorful portrayal of the city's tumultuous history, followed by a stroll through Akihabara, with store after store offering the latest computers, cellphones, cameras, and more. Next, go to Harajuku to see Meiji Shrine, Tokyo's most popular shrine, followed by shopping at Oriental Bazaar, great for Japanese souvenirs. End the day with eye-popping views from the 45th-floor observatory in Shinjuku's Tokyo Metropolitan Government Office, followed by a stroll through Japan's most notorious and craziest nightlife district, Kabuki-cho.
Day 4: Nikko
An excellent choice for a day trip is Nikko, famous for its sumptuous mausoleum of Tokugawa Ieyasu, Japan's most famous shogun, set in a forest of majestic cedars.
Day 5: Takayama & the Japan Alps
Early in the morning, take the Shinkansen to Nagoya (about 2 hr.) and then a 3-hour train ride to Takayama in the Japan Alps (if you don't have a rail pass, there are also direct buses from Tokyo's Shinjuku Station). Explore the picturesque, narrow streets of this old castle town and its many interesting museums and merchants' homes. Since Takayama has more traditional Japanese inns than hotels, this is the perfect place to experience tatami living, with accommodations available at various price ranges.
Day 6: Exploring Takayama
Start your day with a stroll through the Miyagawa Morning Market on the bank of a river. Of the many small museums and attractions in Takayama, must-sees include the Hida Folk Village with its rural architecture, old merchant homes open to the public, and the Hirata Folk Art Museum filled with items used in daily life during the Edo Period (1603-1867). Also not to be missed is the Historical Government House, the only regional administrative building from the shogun era still in existence.
Day 7: Overnight in Shirakawa-go
Take a 1-hour bus ride to Shirakawa-go, where you'll find the village of Ogimachi, a UNESCO World Cultural and Natural Heritage Site with thatch-roofed houses. Several farmhouses are open to the public as museums, but your reason for coming here is to actually spend the night in one.
Days 8 & 9: Kanazawa
Take the bus 1 1/4 hours (available only mid-Mar to Nov) or return to Takayama for the train onward to Kanazawa, famous for its artisans and crafts. It also boasts one of my favorite gardens in Japan, Kenrokuen, several fine art museums, well-preserved former geisha and samurai districts, and Myoryuji Temple (known as the Ninja Temple).
Day 10: Mount Koya
Take an early morning train to Osaka, transferring there for a train and cable car to Mount Koya. Japan's most sacred religious site, Mount Koya is achingly beautiful with more than 115 Buddhist temples spread through the forests. Be sure to take both a day and a nighttime stroll past towering cypress trees and countless tombs and memorial tablets to Okunoin, the burial ground of Kobo Daishi, one of Japan's most revered Buddhist priests. Spend the night in a temple, dining on vegetarian food.
Days 11, 12 & 13: Kyoto
After a vegetarian breakfast and perhaps an early morning Buddhist service, return to Osaka and take the train to Kyoto, where you'll spend the next few days as outlined above in "Japan in 1 Week." If time permits, include an excursion to Nara, an ancient capital even older than Kyoto. Most of Nara's historic buildings and temples, including Todaiji Temple with its Great Buddha, are enclosed within an expansive park that is also home to free-roaming deer.
Day 14: Hiroshima
Take a bullet train bound for Hiroshima. En route, make a stopover in Himeji to see Himeji Castle, easily the most impressive castle in Japan. In Hiroshima, you'll want to head to Peace Memorial Park with its sobering memorials and museum that does an impressive job of detailing events surrounding the explosion of the atomic bomb.