Accomodation
Japan, being one of the most expensive countries in Asia to choose for travel seems to have the same general costliness to its lodging as well. You still have tons of choices in the matter tho.
This is your cheapest option! Do you remember the email address of that cool person who said they were Okinawa-bound at the Tokyo orientation? If you are super friendly and keep in touch with the people you met on the plane, in the hotel or in a workshop, you may end up with accomodation on the cheap in the more exotic places in Japan.
Remember to be prepared to return the favor. Not everyone makes it to Shikoku and there are a few interesting things to check out here. Having friends in Hiroshima, Sapporo, Aomori or Kagoshima could come in very handy when you feel like hitting up one of their spectacular festivals.
Tatami Timeshare is a more formal way of doing the same. Run by National AJET. You submit your name and preferences (female / male, non-smoking etc) and get a list in the Fall with other like-minded JETs. It seems to have fallen out of popularity lately, but if you are willing to put up some folks in exchange for a chance to stay in other areas on the cheap, check out the website at AJET.net. Realize that many ALTs are rural, and there won't likely be many Tokyo/Osaka memebers, but if you want to see "real Japan" in other parts of Japan, it might be worth a try.
CampingIf you have access to a car and a group of willing friends, why not head out camping for the weekend! Camping is cheap and fun way to get outside in Japan. Usually cheap or free during off-season ('Official' season ends in September)! They often have 100 yen showers, running water, BBQ, and if you're lucky an onsen or hot spring! Ask your friends for local sites as most info is usually in Japanese. There is 'right to roam' in Japan on public land. This means you won't get into bother sleeping in parks, on beaches, by the roadside, almost anywhere you care to try to camp. Be careful as some campgrounds may close in September. Camping gear is readily available at hardware shops (DIK etc). JNTO's list of campsites across Japan
Japanese HostelsA relatively cheap option for Japan. Prices usually range from 2,000 to 4,000 yen a night depending on location.
Easily found in large cities, these strange establishments are the result of a hard working
labor force. If you're into sci-fi they're for you. Reservations are usually not needed and you can usually check-in at any time, but on weekends it pays to be safe. They are usually quite cheap, about 3,000 yen.
The capsule hotel in Matsuyama is located in front of Shieki on the 9th floor of the New Ground Hotel Building. With its 2,700 yen a night rate, this is the cheapest hotel you will find in Matsuyama. Tel: 089-945-7089 Fax: 089-933-2801.
More expensive than above, but super clean and well run. If you live out in a rural area, consider getting a membership to one of the larger chains or a hotel in your nearest city. These cards are about 1,000 yen and will save you a bundle when you crash in the city for a night! From about 5,000 yen.
In Matsuyama, the popular ones are the Abis Hotel, the Super Hotel and the Toyoko Inn. Check out their websites for more details.
Ryokan (Traditional Japanese Inn)Ryokan are one of the best
things about traveling in Japan. There are a range of ryokan available, with varying prices – but usually they are expensive. Try to book one if you have friends or family visit for a special treat. The service is exceptional and if you like onsen and traditional Japanese food, you'll love it (even though your wallet won't).
www.japaneseguesthouses.com is a great resource for looking up Ryokan by location and price and an exceptional resource for booking a Ryokan if your Japanese isn't up to snuff.
Many temples in the Kansai area offer temple lodging to visiting tourist. They are a bit expensive, but they offer a genuine experience of the tradition and religion of Japan. The meals served at the temple are shojin ryori, the vegetarian cuisine of monks. At many shukubo, guests have also the opportunity to participate in the morning prayers, which typically start around 6am and last for about 30-45 minutes. For more info, please visit this Japanese listing of Shukubou at http://syukubo.com