Japan Focus has a number of articles that are useful for the course/essays.

http://www.japanfocus.org/

In addition,

On Hiroshima/Nagasaki

‘Remembering the Atomic Bomb’, by P.J. Hill, considers the debate around the decision to drop the A-Bomb.
http://www.nd.edu/~frswrite/mcpartlin98/Hill.shtml

‘The Great Atomic Bomb Debate’ looks at the several viewpoints on the bombings.
http://www.ohiou.edu/perspectives/9701/bomb2.htm

Nagasaki
http://www.exploratorium.edu/nagasaki/journey/journey1.html

This site broadly covers the issue and has numerous links on the A-bombing of Japan.
http://members.aol.com/TeacherNet/Atomic.html#Decision

The A-Bomb WWW Museum.
http://www.csi.ad.jp/ABOMB/

‘The Hiroshima Archive’ is originally set up to join the on-line effort made by many people all over the world to commemorate the 50th anniversary of the atomic bombing.
http://www.lclark.edu/~history/HIROSHIMA/

‘The Atomic Bomb decision’, documents on the decision to use atomic bombs on the cities of Hiroshima and Nagasaki.
http://www.dannen.com/decision/index.html

‘The decision to use the Atomic Bomb’, Gar Alperovitz and the H-net debate.
http://www.doug-long.com/debate.htm