We will leave Japan this summer. Here is a bit of our accumulated knowledge:
General
In Japan, you get what you pay for. We have experienced only one exception to this rule, at a restaurant in Miyazaki. The pricier hotel room is bigger, the pricier meal has more expensive ingredients, the pricier fruit is sweet and ripe. Often it is worth it to pay a bit more, when you know the product is worthwhile.
Buy a couple medium sized cheap towels at the 100Y shop and take them when you travel. They are useful for onsen (to avoid towel rental charges) and cheaper minshukus that don't provide towels. And they dry quickly.
Air travel
Always check to see if Skymark flies to your destination. They are the low-priced carrier in Japan and the service is identical (ie, excellent) to JAL and ANA. At present they go to Fukuoka and Tokyo.
Use hyperedia to help you book a domestic trip. Sometimes it is easier to travel to a nearby city and take the train into your destination than it is to fly directly there. http://www.japanrail.com/JR_hyperdia.html
Accommodations
The business hotel is a great option in cities - they cluster at train stations, you can walk one to the next until you find a decent room and price, the price is reasonable, and you get a Western-style bed and a place to put your stuff. And they almost always have vending machines with cheap beer and other beverages. Downsides are the soullessness and the small rooms.
Ryokan are dressed up minshuku. Although an interesting experience, better value is often found by paying for a nice dinner out on the town and staying at a business hotel or minshuku (whichever is available).
Surviving tatami rooms - if there are multiple futons in the linen cabinet, pile 2 on top of each other, or pile up the comforter on top of the futon. This is probably not community-spirited, but makes a huge difference for your hips and shoulders. Consider carrying a sheet sack if you like sheets. Bean-filled pillows are also less than ideal if you are used to a fluffy pillow. Instead, fold over the end of the futon or wrap the pillow with something soft, or roll up a comforter to use as a pillow.
Food -
Breakfast - major cities have lots of bakeries, some of which discount pastries/bread in the afternoon. Buy a couple on your way back to the hotel after a long day out, and have them for breakfast. Combined with some canned coffee, this is the cheapest and most satisfying breakfast you will find in Japan. If in a minshuku that includes breakfast, be prepared for rice with miso soup and fish - tasty, but hard to stomach for more than 3 days straight.
Eat lunch at cafes, and order the set lunch. Always fun and often quite good, and it removes the language barrier. You typically get tea or coffee included, which typically comes after the meal. In areas with high gaijin traffic, you will often be asked if you want your drink before or after.
Do not eat in "Chinese" diner/restaurants in Japan, no matter how alluringly inexpensive the food is. Just not worth it. Do not order "Chinese" food in izakayas, unless it is gyoza or fried rice which is hard to screw up.
Spanish and French food can be amazing in Japan. Italian is a bit oriented towards pizza and pasta, but the Japanese take on these can be quite tasty. Mexican should be avoided - the ingredients are just not available. We have found some decent south asian food - Indian, Thai - but also some poor interpretations of these complex cuisines.
Dinner in nice restaurants tends to be fairly expensive in Japan. You can often get the same food for half price at lunch. So we tended to avoid going out to dinner in Okinawa, where the izakayas all seem to serve the same food that is not terribly appealing to us. On mainland, we tried to find a small izakaya or bistro for a light meal and a couple drinks.
Desserts in Japan often suffer from the worldwide problem of looking better than they taste. However, in general portion sizes and sugar levels are more reasonable than in the west. And some places have amazing desserts, so is can be worth it to take the splurge.
Beer is the national beverage. An average-sized beer should cost less than 500Y. Shochu mixed with green or jasmine tea is a nice low-cal beverage. Many gaijin do not love awamori but it is decent mixed, ie with Calpis and pink grapefruit juice.
Transportation -
Mainland city to city should be done by train, city to village by train or bus. Some rural areas require a car to maximize the experience. Driving in these areas is generally civilised, although slow-going on local roads if you get behind a truck or old person. We rented a car in Kyushu to visit the mountains and found it quite helpful.
Renting a car in Japan is hassle-free. No one tries to scam you to upgrade, or to buy gas from them, or add on some crazy insurance policy. But it is more expensive than the USA, typically 40-60$ a day. Book ahead with an international rental company like Hertz and they will accept your SOFA licence. Otherwise, you must have a current international drivers license (buy before you leave your home nation).
Renting a moped is hugely advantageous on islands like Iriomote or Zamami. You can get a single person 50cc moped with a car license. A SOFA license is OK in some places, but having an international drivers license is required some places and preferred in many. A two-person moped requires a motorcycle international drivers license so, if you have a motorcycle license then buy the international drivers license from from AAA before you leave.
