which includes more than military personnel:
http://www.geocities.com/ywaciv/bodies.html The list provided there isn't up to date, but you might be able to find more information on some of the links provided onsite.
Military/Intelligence/Defense resignations/dismissals:
RAND BEERS - NATIONAL SECURITY COUNCIL
Rand Beers
ROBERT BLACKWILL - NATIONAL SECURITY COUNCIL
Two national security officials quit Bush's administration
RICHARD CLARKE - DIRECTOR NATIONAL SECURITY COUNCIL/CYBERSPACE SECURITY
Attrition Security Rant
Leslie Stahl interviews Richard Clarke
VICTORIA CLARKE - DEFENSE DEPARTMENT
Pentagon Spokeswoman stepping down - 6/16/03
J.D. CROUCH II - ASST SECRETARY OF DEFENSE FOR INTERNATIONAL SECURITY POLICY
Pentagon Hawk Released – Straws in the Wind? - 10/31/03
KENNETH DeGRAFFENREID - PENTAGON, INTEL
The Gray Zone
GEN. WAYNE DOWNING - DEPUTY NATIONAL SECURITY ADVISER FOR COUNTERTERRORISM
Gen. Wayne Downing: counterterrorism chief resigns - 6/27/02
DOUGLAS FEITH - UNDERSECRETARY OF DEFENSE
Losing Feith
Feith Resigns Under Pressure of Investigations
GEN. TOMMY FRANKS - U.S. ARMY CENTCOM
Rumsfeld Announces Franks' Resignation - 5/23/03
GEN. JAY GARNER
Exclusive interview with: General Jay Garner
CLARK KENT IRVING
Not Mild-Mannered Enough
STEPHEN R. KAPPES - CIA DEPTY DIR OPERATIONS
2 key officials quit in CIA shake-up amid new leadership
DAVID KAY - WEAPONS INSPECTOR
Inspector Calls US Iraq Intelligence a Failure
KAREN KWIATKOWSKI - DoD NEAR EAST BUREAU
Goodbye, Mr. President: the Secret Resignation Letters
ISAM AL-KHAFAJI - IRAQI RECONSTRUCTION COUNCIL
I Did Not Want To Be a Collaborator - 7/28/03
COL. DOUGLAS MACGREGOR - US ARMY
Maverick colonel blames US army's 'sycophantic' culture and heavy-handedness for failures in Iraq - June 9, 2004
JOHN MC LAUGHLIN - DEPUTY DIRECTOR, CIA
Agency Is Said to Be in Turmoil Under New Director Goss
BEN MILLER
FLYNT LEVERETT
HILLARY MANN
Two U.S. Diplomats Resign over Iraq Stance
JAMI MISCIK - CIA ANALYST CHIEF
Chief of CIA's analysts to quit
LT. JOHN OLIVIERA - U.S. NAVY
Navy Public Affairs Officer Who Worked in Iraq Condemns President Bush & The U.S. Invasion
JOHN O'NEILL - FBI*
O'Neill's Life and Career (Dead link replacement)
*See John O'Neill also in Part II - Deaths
JAMES PAVITT - DEPUTY DIRECTOR OF OPERATIONS, CIA
Second top-level resignation at CIA - June 4, 2004
Coup d'Etat
RICHARD PERLE - PENTAGON ADVISORY BOARD CHAIRMAN
Perle Resigns as Chairman of the Defense Policy Board
JOHN M. POINDEXTER - DEFENSE DEPARTMENT
Poindexter to Resign Following Terrorist Futures Debacle - 7/31/03
ANTHONY PRINCIPI - SECRETARY VETERANS AFFAIRS
Heads roll at Veterans Administration
PAUL REDMOND - DEPARTMENT HOMELAND SECURITY
Top Homeland Security Official Resigns Position
Riddle As U.S. Spy Chief Quits
TOM RIDGE - SECRETARY OF DEPARTMENT HOMELAND SECURITY
Ridge Resigns Homeland Post
HOWARD SCHMIDT - CYPBERSPACE SECURITY / NATIONAL SECURITY COUNCIL (see also Richard Clarke)
White House Cybersecurity Adviser Resigns - April 21, 2003
GEN. ERIC SHINSEKI - U.S. ARMY CHIEF OF STAFF
Gen. Eric Shinseki Resigns - 6/10/03
MICHAEL J. SULICK - CIA OFFICE OF DIR OPERATIONS
2 key officials quit in CIA shake-up amid new leadership
GEORGE TENET - DIRECTOR, CIA
Tenet's Perjury And Resignation
Coup d'Etat
LARRY THOMPSON - DEPARTMENT OF JUSTICE
High-level resignation at Justice Department - 8/12/03
Rep. John Conyers Letter Regarding DoJ Handling of Enron (pdf)
Bush Point Man on Corporate Crime Accused of Fraud
THOMAS E. WHITE - U.S. ARMY SECRETARY
Ousted Army Chief Blasts Bush Iraq Policy - 5/03
RABBI DOV ZAKHEIM - PENTAGON CHIEF FINANCIAL OFFICER
Pentagon finance manager resigns
GENERAL ANTHONY ZINNI
General Anthony C. Zinni, USMC
War Over President Bush's Words Heats Up
TWO UNDERCOVER DIRECTORS - CIA
Two More Top CIA Officials Take a Hike