This site contains information for anyone interested Kyoto, Japan. It will be especially good for those who are planning to travel here for extended periods. There is information and tons of links.
The cheapest way to stay in Kyoto (if you can't crash on your friend's floor) is to stay in a guest house. These vary in quality. Please see the following list for contact details, so please ask a lot of questions, and if possible, view the place prior to committing.
Please note that the periods mid-March to mid-May and October through November are the peak tourist seasons in Kyoto. It may be difficult to secure lodging at your first, second or even third choice of guest house. Additionally, many of the better guest houses fill up quickly with medium to long term residents who prefer the convenience and lower costs of group living over the more isolated, more expensive option of renting an apartment (mansion) in Japan.
Ebisu's Kyoto: located near Kyoto University on a lovely hill. Small house (only 8 single rooms), and minimum stays of one month. 30 min. by bus #206 from Kyoto Station A2 terminal to "Konoe Doori" bus stop
You could try Tour Club, near Kyoto Station. They seem to keep it nice and clean...
There's a new one, also near Kyoto Station ... J-Hopper's.
Or, near Toji, just south of Kyoto Station, is Tojian.
Near Kawaramachi Marutamachi (a 20 minute bus ride from Kyoto Station, is Uno House.
Or you could try:
I.S.E. Dorm (No home page)
10 Higashi-fukunokawa-cho, Okazaki, Sakyo-ku, Kyoto
Tel: (075) 771-0566
30 min. by bus #206 from Kyoto Station A2 terminal to "Kumano Jinja mae" bus stop
Tani House (No home page)
8 Daitokuji-cho, Murasakino, Kita-ku, Kyoto
Tel: (075) 492-5489 Fax: 252-3277
45 min. by bus #206 from Kyoto Station B4 terminal to "Kenkun jinja mae" bus stop.
And yet another:
English Guest House - Downtown Annex (No home page)
114-8 Suziya-cho, Tominokoji-dori, Bukkoji-sagaru, Shimogyo-ku, Kyoto
Tel: (075) 722-0495 FAX: 344-2534
5 min. by subway from Kyoto Station to "Shijo" station and 5 min. walk.
Tani Guest House (No home page)
13, Inoguchi-cho, Kisshoin, Minami-ku, Kyoto
Tel: (075) 681-7437, 671-2627 (Owner 341--1344)
5 min. by JR from "Kyoto" to "Nishioji" station and 10 min. walk
Or, up north, is GreenPeace. Take the subway from Kyoto Station to Kitayama Station, then a short walk.