I second the recommendation on Koyasan. It's been many years since I visited Koyasan but I still have fond memories of the experience.

You can find several threads here on Flyertalk by searching on Koyasan or Koya (Mt. Koya). Here are some other sites you can check out:

http://www.shukubo.jp/eng/index.html
http://www.japan-guide.com/e/e4900.html
http://wikitravel.org/en/Mount_Koya