5. American Guerrilla: My War Behind Japanese Lines, Roger Hillsman
4. In Our Image: America's Empire in the Phillippines, Stanley Karnow
3. Armageddon: The Battle for Germany, 1944-1945, Max Hastings
2. John Adams, David McCullough
1. Team of Rivals: The Political Genius of Abraham Lincoln, Doris Kearns Goodwin
Numbers 3 to 5 are excellent books that help put current conflicts like the war in Iraq in a healthier historical context than most people, both for and against the war, frankly have. Numbers 1 and 2 I would commend for their warm and moving accounts of two great (if unappreciated, in the case of Adams) presidents and their relationships with other famous men (Jefferson, in the case of Adams, and William Seward, in the case of Lincoln).
Honorable mentions that didn't make my Top 5 are Freedom & Virtue: The Conservative/Libertarian Debate by George Carey and The Future of Freedom: Illiberal Democracy at Home and Abroad by Fareed Zakaria. The latter, in particular, I would commend to anyone who believes that democracy is an unqualified good that can work anywhere.
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One book I found a little disappointing was Six Days of War: June 1967 and the Making of the Modern Middle East by Michael Oren. It was informative and worth reading for anyone who needs more proof about how utterly dysfunctional Arab states really are, but not as gripping an account of combat as I had hoped.
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The rest of the non-fiction books I recall reading in 2006 were:
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1776, David McCullough
In the Company of Soldiers: A Chronicle of Combat, Rick Atkinson
Martin Luther, Martin Marty
Plan of Attack, Bob Woodward
The Victors: Eisenhower and His Boys: The Men of World War II, Stephen Ambrose