NewsOnJapan.com: Providing unmatched daily news coverage on topics of business, economy, internet, politics, society, stock market, and technology.

Japanese Newspapers/News Agencies

Nikkei Net Interactive: Rating: 5/5 A great, well laid out, one stop site for timely news on Japan and Asia. Includes simple keyword search with advanced search planned for the future.
Kyodo News: Rating: 4/5 A bit of a plain and shallow site, but very up-to-date. (Recommends reloading every 15 minutes to get latest headlines!). Advanced search includes photograph search.
The Daily Yomiuri: Rating: 3.5/5 Unfortunately this site's new face is less attractive than the old one. Half your page is permanently taken up by an empty frame! They've made an effort and definitely win points for content (see the editorial, column, weekend and features sections), but I can't help disliking the presentation.
Japan Times: Rating: 3.5/5 Not focused on headline news but wins points for additional interesting content from the print edition. Archive is useful but not searchable. They've been promising for years to include their classifieds on-line, but have shown no sign of actually doing so.
Mainichi News: Rating: 2.5/5 Jazzy appearance with limited news but does have a few other interesting pages.
Asahi English News: Rating: 2/5 OK for headline news (go down too Asahi News icon for more headlines), but little additional interesting content.

World Sources: Japan

NewsIndex: Keywords - Japan OR Japanese
Asiaweek Newsmap: Japan

World Sources: Asia Pacific

BBC Asia Pacific News
CNN Asia-Pacific News

Online News: Enter Japan, Japanese etc. in the Keyword search!