Disclaimer: This list is not complete or up-to-date. I have long been collecting these kinds of anecdotes to motivate our own fault-tolerance research, and wanted to make them available to others. Please email me if you know of any that I am missing.

OUR SURVEYS
Causes of Failure in Web Applications Soila M. Pertet and Priya Narasimhan, Technical Report PDL-CMU-05-109, Carnegie Mellon University, December 2005

UPGRADE-RELATED FAILURES
Failed Windows XP upgrade downs 60,000 UK Goverment PCs, November 2004
Vonage voicemail vanishes during site upgrade, July 2005
MCI upgrade glitch disrupts ATM service, August 1999
Software upgrade glitch grounds Los Angeles airport, October 2000
EDS: IT upgrade caused software glitch at UK agency, December 2004
The truth: What caused the AT&T frame relay network outage, February 2001
Upgrade glitch downs AT&T Wireless' CRM system, November 2001
eBay says system upgrade tied to recent outages, October 2000

E-COMMERCE SYSTEM FAILURES
Schwab Outage: IT Wake-Up Call, InternetWeek, February 26, 1999
Stock Market Outages Highlight Software Availability Issues, The Payne Report, July/August 2001
Outages at eBay:
    -- eBay Retrenches, InternetWeek, June 17, 1999
    -- eBay Servers Go Down -- Again, InternetWeek, June 30, 1999
    -- eBay Crashes Again, InternetWeek, August 9, 1999
    -- eBay goes back online after prolonged outages, CNET News.com, January 4, 2001
Outages at E-Trade:
    -- E-Trade Suffers Outage, InternetWeek, February 3, 1999
    -- Another Outage at E-Trade, InternetWeek, Feburary 4, 1999
    -- E-Trade Explains Cause of Last Week's Outage, InternetWeek, February 10, 1999>
    -- E-Trade CIO Discusses the Outages, InternetWeek, February 10, 1999
Points of Reference: e-Commerce Failures, Online Brokerage Industry Report, 1999

MISSION-CRITICAL SYSTEM FAILURES
Humming along with technology, until it's not, Washington Post, November 5, 2009 (computer failure disrupting 750 traffic lights)
Human error called culprit in 3 rocket launch failures, Florida Today Space Online, June 16, 1999
Ariane 5 Flight 501 Failure, Inquiry Board Report, Prof. J. L. Lions, July 1996
Electric Blackout of August 2003 in Northeast US and Canada:
    -- Reports from the North Americal Electric Reliability Council
    -- Reports from the US Department of Energy
Therac-25 radiation incidents:
    -- Investigation of the Therac-25 accidents, Leveson & Turner, July 1993
    -- Therac-25 case materials, computingcases.org
Navy Smart Ship USS Yorktown:
    -- The Smart Ship is not the answer, U.S. Naval Institute Proceedings, June 1998
    -- Software glitches leave Navy Smart Ship dead in the water, Government Computer News, July 13, 1998.

MISCELLANEOUS
Netcraft News and Surveys
Slashdot stories on bugs, viruses and downtime