Here is a "best of" of Japanese politics in the news over the last 10 years classified by topic. Many online articles have disappeared over the years. These are those that are still available.
Domestic politics
Japan Times : LDP panel eyes changes to Constitution preamble (April 2004)
Japan Times : Constitutional changes eyed to let female on throne, legalize military (November 2004)
The Age : Rewriting an ugly past (August 2005)
Washington Post : The Rise of Japan's Thought Police (August 2006)
Foreign policy
Japan Times : Japan plods path of isolation (January 2003)
Bloomberg :Japan May Need to Rethink Interment of Yasukuni's War Criminals (May 2005)
BBC News :Japan air force chief faces sack (October 2008)
Japan-China relations
CNN : Rented islands strain Sino-Japanese relations (January 2003)
Japan-Korea relations
Japan Times : Tokyo, Pyongyang trade accusations as talks commence (October 2002)
The Age : Japan may ask US to strike (January 2003)
Japan-US relations
GEN. CURTIS LEMAY
'The executioner of Tokyo'
MOFA : The 2002 Opinion Survey on the Image of Japan in the U.S. (2002)
Various
The World Traveler : Why Japan Remains a Threat to Peace and Democracy in Asia (2004)
Japan Times : GEN. CURTIS LEMAY - 'The executioner of Tokyo' (March 2005)
TIME : The God-Emperor
