I spent ~48 hours on the way back to the United States from a six week trip in Thailand, Vietnam, Cambodia, and Laos. Japan could easily be a six week trip on its own.

Major Events: Cherry Blossom Festival (early spring), religious festivals (various), New Years.

Tokyo is divided into 23 wards, with Chiyoda at the core. This district includes Tokyo Imperial Palace, Tokyo Station (central train station), and several large business offices.

Nav:

Tokyo Imperial Palace: The home of the Emperor of Japan.

Shibuya Scramble: Famed crosswalk in the Shibuya ward, about 25 minutes from Chiyoda by metro.

Other Notable Attractions:

Tokyo National Museum: A great place to get an overview of the of the Japanese people, culture, and history.

Ginza District: Shop till you drop!

Day Trips:

Mount Fuji: If you want to see it, hop the train and head out. If you want to hike, its not a day trip and you should be properly prepared for the climb. Open season is roughly July through September.

Kyoto: My opinion is Kyoto is too far for a day trip, even with high speed rail. Stay overnight or burn the midnight oil with an early arrival and late departure if it's essential.

Nosh:

Ittouya Kayabacho: Ramen house. You put money into a machine, get a ticket for the items you selected, then sit down and wait for your order to come up. Tables or the bar have all the condiments you need (chili oil, garlic, soy sauce, etc).

Nihonbashi Sushikou: A great offering from the chef/owner, who speaks great English so he can help you with menu questions. The place was owned by his father before him. Try one of the sushi combos (like I did) or go all out for omakase style, where the chef picks the menu for you (which is what I wish I would have done).

Nip:

Sake: A trip to Japan is NOT complete without sake. The rice wine is a staple in the country.

Whisky: Suntory is the internationally exported whisky. It's worth a try. The World Whisky is a blend of Irish, Scotch, American, Canadian, and Japanese whiskies...so it has a bit of a peat to it but mellowed by the North American whiskies.

Plum Wine: Waaaayyyy too sweet for my palate. Tried it and didn't finish a small pour. If you like moscato, it may be up your alley.