Japan hotels
In addition to the usual youth hostels and business hotels, you can find several kinds of uniquely Japanese accommodation, ranging from rarefied ryokan inns to strictly functional capsule hotels and utterly over-the-top love hotels.
When reserving any Japanese accommodations, bear in mind that many smaller operations may hesitate to accept foreigners, fearing language difficulties or other cultural misunderstandings. This is to some extent institutionalized: large travel agency databases note which (few) hotels are prepared to handle foreigners, and they may tell you that all lodgings are booked if only these are full! Instead of calling up in English, you may find it better to get a Japanese acquaintance or local tourist office to make the booking for you. Alternatively, for cheap Internet rates, Rakuten's English search tool is an invaluable utility.
When checking in to any type of accomodation, the Japanese are, by law, required to make a copy of your passport. It is a good idea, especially if you are travelling in groups, to present the clerk a photo copy of your passport to speed up check-in. Aside from this, remember that Japan is mostly a cash only country, and credit cards are usually not accepted in smaller forms of accomodation, including, but not limited to, small business hotels. Bring enough cash to be able to pay in advance.
One thing to beware in wintertime: traditional Japanese houses are designed to be cool in summer, which all too often means that they are freezing cold inside in winter. Bulk up on clothing and make good use of the bathing facilities to stay warm; fortunately, futon bedding is usually quite warm and getting a good night's sleep is rarely a problem.