"Four black dragons, spitting fire,
And the earth trembled, and the sky cracked,
And I thought it was the end of the world."

"And it was."

-exchange between two characters at the begiinning of Stephen Sondheim's Pacific Overtures, describing the arrival in Japan of Commodore Perry's "Black Ships"

My Ten Rules for Affordable Travel to Japan are:

1. When to go: The best time seems to be September or October. June, July, and August (especially) are very busy times and hard to get cheap airfares for. May is cherry-blossom time and probably just as bad. December is also busy.
2. Guide books: The Lonely Planet has the best information on hotels and getting around. Contact the Japan National Tourist Organization and get their brochures, including maps of Tokyo, Kyoto, and Japan. Stop in their offices in Tokyo and/or Kyoto for lots of useful pamphlets and information.
3. Airfare: Shop around. The "bucket shops" (ticket consolidators who place ads in the back of major city's newspapers' Sunday travel section are a good place to start, as well as on-line search engines such as kayak.com and mobissimo.com.
4. Long-distance ground travel: Rail is the way to go, but it's expensive. Get a JapanRail Pass, but maximize its use by compacting all your long-distance travel. If you are doing a Tokyo-Hiroshima-Kyoto loop in some form within a seven-day period, the one-week pass is cheaper. If you are going to Tokyo and Kyoto, being able to fly into one and home from the other will save you a couple of hundred dollars in ground costs getting back. (Tokyo uses Narita Airport; Kyoto uses Osaka's Kansai Airport.) The Rail Pass does not allow use of some of the fastest trains, though.
5. Local ground travel: Learn the subways and buses; taxis are expensive and the cities are too spread-out to walk. The Tokyo subway system is very simple, and color-coded (for those rare stations where you can't find a map labeled in romanji).
6. Hotels [as of 1996]: You can get reasonable double rooms for around US$75/night Singles are cheaper, or you can try youth hostels for even less if you don't mind all the rules. Reserve ahead; given that no one seems to require a deposit, it's probably safer to line up your rooms before locking in your plane ticket. (Note: all the cheaper places seem to be Japanese-style beds-futons on the floor-though with Western toilets. If you can't sleep on the floor, it will cost you.)
7. Eating: Your best bets are the restaurants with plastic food in the window with prices on it. Bring a pad of paper and just copy the symbols next to what you want, then give the paper to the person inside--much easier than dragging them out to the street to point to it. (If you have a digital camera, you can use that instead.) Learn the Japanese characters for the numbers; a lot of places show prices that way. Cheap dishes include noodle soups, pork cutlets, some Western dishes, and even sushi. Any restaurant where people are eating with forks and knives is probably expensive; stick to those which use chopsticks. Large department stores often have food departments where you can buy take-out sushi by the piece. We averaged about US$35/day each for food, including all snacks, beverages (see below), etc.
8. Drinking: Beverages such as sodas and coffee cost about three times as much in a restaurant as from the ubiquitous street vending machines (US$3 versus US$1). To save money, stick to the machines. (Bring a bandana to hold the hot can of coffee after it comes out!) Restaurants serve water or small cups of tea, or both, free with meals. "Coffee shops" are even more expensive than restaurants (US$5 a cup).
9. What to bring: Not much-you'll be carrying your own luggage through big train stations and such. Bring comfortable shoes. You will be on your feet a lot. In the fight between "comfortable" and "easy to take off at the door," comfortable should win. (Bring a shoe horn if that helps. Make sure your socks do not have holes!) A compass is useful (especially in finding your way around large department stores), and not something everyone thinks to bring. Bring a fork if you must use one.
10. Money: Bring travellers cheques. There are ATMs, but they are not usually on networks like Plus or Cirrus (the one at Narita Airport is), and most don't take North American bank cards, or have prompts in English. Cash advances against credit cards can cost a bundle in finance charges unless you pay the money in first to create a credit balance. (This does not apply to debit cards.) Very few (cheap) places take credit cards (or debit cards).

Our cost break-down for a three-week trip for two people in 1996:

Airfare	US$1959
Ground Transportation	786
Hotels	1361
Meals	567
Film/Developing	219
Miscellaneous	527
Total	US$5409

"Nippon, the floating kingdom.
There was a time when foreigners were not welcome here
but that was long ago-a hundred and twenty years.
Welcome to Japan."
-the end of Stephen Sondheim's Pacific Ovvertures (1973)

Full travelogue at http://www.travel-library.com/asia/japan/leeper.html.

Suggested reading:

• Daniel George, Japan (Travelers Tales)
• Shifra Horn, Shalom, Japan (Kensington)
• Japan (Lonely Planet)