I've checked and updated the broken links from the criticism section of John Negroponte's Wikipedia page, and fixed them in Wikipedia too:
https://en.wikipedia.org/wiki/John_Negroponte#Criticism
We Must Not Move On (Paul Laverty for The Guardian, April 13, 2005)
https://www.theguardian.com/comment/story/0,3604,1458142,00....
Negroponte's Time in Honduras at Issue (Michael Dobbs for The Washington Post, March 21, 2005)
https://web.archive.org/web/20110629054237/https://www.washi...
John Negroponte's Human Rights Record Continues to Stir Debate (May I Speak Freely Media - extensive list of links to critical commentary and news articles, etc., February 2005)
https://web.archive.org/web/20041113133759/http://www.mayisp...
Bush hands key post to veteran of dirty wars (Duncan Campbell of The Guardian on Negroponte's past history, February 18, 2005)
https://www.theguardian.com/international/story/0,3604,14170...
From Central America to Iraq (Noam Chomsky for Khaleej Times, August 6, 2004)
http://www.chomsky.info/articles/20040806.htm
Our man in Honduras (Stephen Kinzer for The New York Review of Books, September 20, 2001)
http://www.nybooks.com/articles/14485
1995 Four-Part Series on Honduras in the 80s (The Baltimore Sun, June 11, 1995 – June 18, 1995)
https://web.archive.org/web/20110629024115/http://www.baltim...
A carefully crafted deception (Ginger Thompson and Gary Cohn for The Baltimore Sun, June 18, 1995)
https://web.archive.org/web/20040427182804/http://www.baltim...
Negroponte Makes the Most of His Post as Minister Without Portfolio (Jeff Stein for Congressional Quarterly, March 3, 2006)
https://web.archive.org/web/20060519110853/http://public.cq....