Kobe University Database of Newspaper Clippings Relating to Industry   http://www.lib.kobe-u.ac.jp/sinbun/
From Meiji to WW2-- this is very specialized, but if you are researching the history of technology/commerce it could be invaluable.

NDL Index of Japanese Newspapers   http://sinbun.ndl.go.jp/
全国新聞総合目録データベース Searchable database for finding out Japanese library holdings for regional and national newspapers; includes information on range of holdings and library contact information.

Newspaper articles on Koreans living in Japan before the war   http://www.zinbun.kyoto-u.ac.jp/%7Emizna/shinbun/
戦前日本在住朝鮮人関係新聞記事検索 Citations but no articles. This database has almost 30,000 items. It is maintained by Mizuno Naoki at Kyoto Daigaku.