Links to finding accommodation all over Japan

http://www.jalan.net - in Japanese only

http://travel.rakuten.co.jp/ - in Japanese only

http://travel.rakuten.co.jp/en/ - in English, but maybe not the same deals available on both

http://www.tokyo-hostel.com - has links to accom all over Japan - in English

http://www.jyh.or.jp - find youth hostels all over Japan. You don't need to be a member to stay, but you'll be charged extra. You can find information on the Japan Youth Hostels website English page, but online registration can only be done on the Japanese version. Youth hostels in Japan are all very different, from strict dormitory style, to the feel of a modern home with western beds, to older traditional buildings. Generally YH are separated by gender. If you're travelling with a partner, unless you're married, you'll probably have to sleep in separate rooms (although occasionally you'll come across a manager who isn't so strict).

http://www.toyoko-inn.com/eng/ - clean, quiet, and simple. Book directly with the hotel online in English. Doubles are about ￥8000 per room/night (not per person). They are centrally located and convenient. Usually include buffet style breakfast.

http://www.verymuch.org/yasuiyado/yasuiyado05-06.html - only in Japanese but has a complete list by prefecture of cheap accommodation

http://www.japanhotel.net/ - business hotels anywhere in Japan. Prices are pretty reasonable and are usually per room not per person. You can also book online in English. Each hotel listed also has a map and directions.

http://japanhotelsonline.net/index.php?tc=9031Q - completely in English

http://www.superhotel.co.jp - reasonable business hotels in main Japanese cities. Only in Japanese.

http://www.jpinn.com - Japan Welcome Inn Group website. Book accommodation in English all over Japan.

http://japaneseguesthouses.com/prefecture.htm - in English, helps you find Ryokans all over Japan.

http://www.jcha.or.jp/english - The Japan City Hotel Association site is pretty good. You can make reservations on line in English

http://www.jnto.go.jp/a-search/search/search_form.php - the accomodation search on the Japan National Tourist Office website is good. It lists hotels and ryokans from a number of different hotel searching sites. You can book in English too.

http://www.itcj.jp/ - a registry of accommodations that can speak English and charge ￥8,000 or less per night. Each listing gives a brief blurb about the place and it's location/atmosphere.

http://www.sotozen-net.or.jp/kokusai/list.htm - lists contact information for many of the zen temples in Japan that allow overnight stays.

Homestay:

A link finding host families in prefectures as far ranging as Gifu or Kagoshima. Usually, you must apply at least one month in advance. http://www.jasso.go.jp/study_j/documents/HomestayHomevisit.pdf

Ecotourism:

Want to stay in an ecolodge? -http://www.ecolodge.gr.jp/index_english01.htm - English page

http://www.ecotourism.gr.jp - Japanese only