Accommodation

There are loads of options for where to stay in Japan. It ranges from the relatively cheap to the immensely expensive, depending on where you want to live, what condition the place is in, and how large the room(s) are/is.

1. You could do it the Japanese way and get a proper apartment

The size of an apartment is judged by how many rooms there are, and what facilities are included. For example, a 1LDK apartment will have one room with a living area, dining area and kitchen, with a separate bathroom. A 2LDK will have two rooms with a living area, dining area and kitchen etc.
This is how you will see apartments advertised.

Pros:
- you get a permanent place to stay
- you can furnish it how you like

Cons:
- it's expensive (key money is everything you pay your landlord before you even move in - can be up to 6 months' rent)
- it's a complicated process (competent knowledge of Japanese would be required!)
- there may be discrimination against dealing with a foreigner
- you will have to get your own furniture etc.

2. You could stay in a hotel

This is only a really viable option if you plan to stay there for a short time, as your bill at the end of it could be astronomical. But you don't have to stay in the Tokyo Park Hyatt, you could find cheaper options, for example, Sakura House's Sakura Hotel in Jimbocho, Tokyo. Of course, there are even cheaper hotels outside of the major cities, Tokyo is bound to have the most pricey. There is also a new hostel (Tokyo's largest) in Asakusa with 162 beds.
Osaka - http://www.asiarooms.com/japan/osaka.html, http://www.travellerspoint.com/budget-hotels-en-ci-921.html
Kyoto - http://www.travellerspoint.com/budget-hotels-en-ci-645.html, http://www.hotelclub.net/hotel.reservations/Kyoto.htm

Pros:
- all utilities paid for
- furnished rooms

Cons:
- expensive!

3. You could stay in a guesthouse, or gaijinhouse (foreigner house)

There are several different types of guesthouse. You could stay in a dormitory, where you share a room with other people. This is probably the cheapest accommodation you will find from ¥35,000. Sakura House seems to be a good choice.

Or, the one that I chose, Sakura House's guesthouse. You rent a room for a month at a time (all utilities etc. included) and share your kitchen, bathroom and toilet with the other occupants of the house. The actual houses can range from tiny old-style Japanese houses in the suburbs to towering high-rise blocks in central Tokyo. The rent can range from ¥48,000 to over ¥100,000 plus a deposit of ¥30,000 when you move in, ¥20,000 of which is refundable when you move out.

You can search by location, price and availability to find accommodation but this seems to be a more difficult way to it.
The easiest way to book a room, at least from what I can see, is using Sakura House's Advance Reservation form where you can ask for a particular date and specify location and your personal requirements if you want and they find available accommodation that suits you. One fault with this system is that you are meant to be able to say 'Other, or anywhere is ok' in relation to where you would like to stay. However, when I tried to submit my application it said that I hadn't specified a location. So I rang them up and asked what I should do. Very helpful man in Shinjuku told me that I just tick any box and then use the requests/ comments box at the end of the form to say that anywhere is fine.

Earlier today, I got an email with an offer of a very nice looking room in central Tokyo to which I replied "Yes! Yes, I'll take it!" They should send me another email asking for my card details (you can only use Visa or MasterCard) to send my deposit and make the reservation official.

You can contact them at info@sakura-house.com or on +81-3-5330-5250 (remember that the + stands for different things in different countries, in the UK it is 00) but remember about the time difference! Tokyo is 9 hours ahead of London and they are open from 8.50am til 5.50pm.

Pros:
- huge variety of choice with Sakura House
- relatively cheap
- good way to meet people
- widespread across Japan
- easy for travelling, especially for people on Working Holiday visas, like me
- fully furnished and utilities are included

Cons:
- usually booked for whole months at a time
- based mainly in major cities
- less privacy than apartments, shared kitchen and bathroom facilities

Sakura House is only based in Tokyo but there are other companies for different cities.
Osaka - http://www11.ocn.ne.jp/~otomari/oig/, http://www.learn4good.com/hostels/budget_accommodations/japan/osaka_international_guesthouse.htm, http://www.u-en.net/english.html
Kyoto - http://www.budgetinnjp.com/, http://www.gojo-guest-house.com/, http://www.kyotojp.com/kyotoguesthouse.html
Nagoya - http://www.freebell.co.jp/GH/
Fukuoka - http://www.a1tourism.com/japan/fukuoka.html, http://www.hostelscentral.com/city-1620.html
Sapporo - http://www.plaza-sapporo.or.jp/sgh/, http://coe.math.sci.hokudai.ac.jp/sympo/venue_g.html

There are others of course, if in doubt, consult google!