If you look at a guidebook of Kyoto, you may find only high price hotels .
But there are many cheap "Weekly Apartment", "Guest House" and "Gaijin House" available.
Weekly apartment has grown in number in big cities including Kyoto, Osaka and Kobe.
Most of them are clean and cheap place to stay.
Especially if you stay in Kyoto with your friends, weekly apartment would be a cheapest place to stay.
Though, meals are not provided usually, there are a few services such as wireless LAN. Also different types including only the kitchen, or kitchen and bathroom.

Higashiyama IVY
2 beds, 3 nights ¥16,400 per room
(¥8,200 per person for 3 nights)
(less than ¥2,800 per person for a night)
4 beds, 3 nights ¥24,800 per room
(¥6,200 per person for 3 nights)
(less than ¥2,100 per person for a night)
If you stay longer than 1 week, you can get more discounts.
For more information:
Address: 90 Yoshino-cho, Higashiyama-ku, Kyoto City
Tel: 075-551-1125 (business hour: 7:00-20:00)
Fax: 075-551-1140

Shukubou is an inn in Temple.
Ninnaji-temle is known as the head temple of Buddhist sect.
You would understand what Buddhist is rather than just reading a book about it.
Ninnaji-temple is close to Ryoanji-temple which is famous for "Karesansui", Japanese dry landscape gardens exhibit sophisticated visual designs with minimal compositions and engender a calm, contemplateive atmosphere.
By staying at Omuro Kaikan and visiting Ryoanji-temple, you can have a "Kyoto" weekend.

Omuro Kaikan in Ninnaji Temple
Address: Mimuro Ouchi33, Ukyo-ku, Kyoto City
zip code 616-8092
Price: ¥4,000/night without meal
¥4,800 with breakfast
¥8,000-¥12,000 with dinner & breakfast
Hanami (花見, lit. "flower viewing") is the Japanese traditional custom of enjoying the beauty of flowers, "flower" in this case almost always meaning cherry blossoms (Jp. sakura), or also ume blossoms (sometimes called "apricot" or "plum").

Walkerplus provides info in Japanese only but still you can enjoy pictures.
It is sometimes difficult to get local info and overview of Japan.
Japan National Tourist Organization provides over view of Japan including beautiful pictures of catsles and scenery and statistics.
Definitely one of the biggest web site which provides tourist info.

If you live in Osaka or planning to move in Osaka, you can have a look at Osaka Visitor's Guide

See also
Kyoto Prefecture Tourism Federation
Hyogo International Tourism Guide
Nara Prefecture Turism Info "Yamatoji Archives"
Shiga Prefecture Turism Info
Wakayama Prefecture Turism Info