General

Japanese Historical Text Initiative http://sunsite.berkeley.edu/JHTI/
Includes 15 texts ranging from the Kojiki to Meiji laws in a searchable database. Also provides a dictionary of basic Shinto terms, a bibliography, and linked electronic texts concerning matsuri, folk religion in Japan, and new religions.

Kyoto University Library Electronic Library   http://edb.kulib.kyoto-u.ac.jp/exhibit/index.html
Includes materials ranging from Nara e-hon to WWII newspapers to modern educational wallcharts.

National Archives of Japan Digital Gallery  http://jpimg.digital.archives.go.jp/kouseisai/index_e.html
Includes documents, maps, scrolls, drawings, photographs and posters. Browsable by category and by keyword.

Waseda's Collection of Chinese and Japanese Classics  http://www.wul.waseda.ac.jp/kotenseki/index.html
Contains Edo era literature, rangaku, the Okuma Shigenobu collection, an exhibition of Edo and Meiji photographs, portraits, newspapers and nishikie from Bakumatsu and Meiji.