Partial list of CIA digraphs, cryptonyms and probable definitions:

AE: Soviet Union
AM: Cuba
BE: Poland
CK: Soviet Union
DI: Czechoslovakia
DM: Yugoslavia
DN: South Korea
ES: Guatemala
GT: Soviet Union
IA: Angola
KU: Part of CIA
LI: Mexico
MH: Worldwide operation
MK: Projects sponsored by the CIA's Technical Services Division
OD: Other Department
PB: President Board
SD: Iran
SM: United Kingdom
TU: South Vietnam
ZR: Normally prefixes the cryptonym for an intelligence intercept program. Seems to go with Staff D ops, Staff D being the group that worked directly with the NSA. Staff D was where ZR/RIFLE, a Castro assassination plot, was buried.

Operations and Projects

ARTICHOKE: Anti-interrogation project. Precursor to MKULTRA.
AQUATONE: Lockheed U-2 Spy Plane Project
BLUEBIRD: mind control program
CHALICE: Lockheed U-2 Spy Plane Project
CHERRY: Covert assassination / destabilization operation during Vietnam war, targeting Prince (later King) Norodom Sihanouk and the government of Cambodia. Disbanded.
CONDOR: 1970s CIA interference in Latin American governments, some allege in the coup and assassination of Salvador Allende in Chile
CORONA: Satellite photo system.
DBACHILLES: 1995 effort to support a military coup in Iraq.
ECHELON: worldwide signals intelligence and analysis network run by the UKUSA Community.
GUSTO: Project to design a follow-on to the Lockheed U-2 Spy Plane
HTAUTOMAT: Photointerpretation center established for the Lockheed U-2 Spy Plane Project
HTLINGUAL: Mail interception operation.
IAFEATURE: Operation to support UNITA and FNLA during the Angolan civil war.
KEMPSTER: Project to reduce the radar cross section (RCS) of the inlets of the Lockheed A-12 Spy Plane
LINCOLN: Ongoing operation involving Basque separatist group ETA
LPMEDLEY: Surveillance of telegraphic information exiting or entering the United States
MHCHAOS: Surveillance of antiwar activists during the Vietnam War
MKDELTA: Stockpiling of lethal biological and chemical agents, subsequently became MKNAOMI
MKNAOMI: Stockpiling of lethal biological and chemical agents, successor to MKDELTA
MKULTRA: Mind control research. MKULTRA means MK (code for scientific projects) and ULTRA (top classification reference, re: ULTRA code breaking in WWII. Renamed MKSEARCH in 1964
MKSEARCH: MKULTRA after 1964, mind control research
MKOFTEN: Testing effects of biological and chemical agents, part of MKSEARCH
OAK: Operation to assassinate suspected South Vietnamese collaborators during Vietnam war
OXCART: Lockheed A-12 Spy Plane Project
PAPERCLIP: US recruiting of German scientists after the Second World War
PHOENIX: Vietnam covert intelligence/assassination operation.
PBFORTUNE: CIA project to supply forces opposed to Guatemala's President Arbenz with weapons, supplies, and funding; predecessor to PBSUCCESS.
PBHISTORY: Central Intelligence Agency project to gather and analyze documents from the Arbenz government in Guatemala that would incriminate Arbenz as a Communist.
PBSUCCESS: (Also PBS) Central Intelligence Agency covert operation to overthrow the Arbenz government in Guatemala.
RAINBOW: Project to reduce the radar cross section (RCS) of the Lockheed U-2 Spy Plane
SHERWOOD: CIA radio broadcast program in Nicaragua begun on May 1, 1954.
THERMOS: Unclassified codeword used in lieu of RAINBOW
TPAJAX: Joint US/UK operation to overthrow Mohammed Mossadeq, Prime Minister of Iran
TSS: Technical Services Staff
WASHTUB: Operation to plant Soviet arms in Nicaragua

Organizations

KUBARK: CIA Headquarters
KUCAGE: CIA Overseas Paramilitary / Propaganda Operations
KUCLUB: Office of Communications
KUDESK: Counterintelligence department
KUDOVE: Office of the director
KUFIRE: Intelligence
KUGOWN: Propaganda
KUHOOK: Negotiations/Logistics (unsure)
KUSODA: CIA Interrogators
ODACID: State Department / US Embassy
ODEARL: US Department of Defense
ODENVY: FBI: Federal Bureau of Investigation
ODOATH: US Navy
ODUNIT: US Air Force
ODYOKE: US Government
QKFLOWAGE: United States Information Agency
SKIMMER: The "Group" CIA cover organization supporting Castillo Armas.
SGUAT: CIA Station in Guatemala
SMOTH: British Secret Intelligence Service (also known as MI6)
SYNCARP: The "Junta," Castillo Armas' political organization headed by Cordova Cerna.
UNIFRUIT: United Fruit Company

Persons

AEFOXTROT: Yuri Ivanovich Nosenko, a Soviet defector
AELADLE: Anatoliy Golitsyn, a Soviet defector
AMLASH: Rolando Cubela Secades, a Cuban official involved in plot to kill Fidel Castro in 1963
AMQUACK: Che Guevara, Argentinian guerrilla leader
AMTHUG: Fidel Castro, president of Cuba
ESQUIRE: James Bamford, author of "The Puzzle Palace"
GPFLOOR: Lee Harvey Oswald, J.F. Kennedy's assassin
GPIDEAL: John F. Kennedy, US president
GRALLSPICE: Pyotr Semonovich Popov, Soviet defector
JMBLUG: John S. Peurifoy, U.S. Ambassador to Guatemala
KUMOTHER: James Jesus Angleton, head of the CIAs counter intelligence
PANCHO: Carlos Castillo Armas, President of Guatemala, also RUFUS
RUFUS: Carlos Castillo Armas, President of Guatemala, also PANCHO
SKILLET: Whiting Willauer, U.S. Ambassador to Honduras.
STANDEL: Jacobo Arbenz, President of Guatemala

Places

BOND: Puerto Barrios, Guatemala
DTFROGS: El Salvador
HTKEEPER: Mexico City
HTPLUME: Panama
JMMADD: CIA airbase near city of Retalhuleu, Guatemala
JMTIDE: CIA airbase in Puerto Cabezas, Nicaragua
JMTRAX: CIA covert airbase/training camp in Guatemala
JMWAVE: CIA station in Miami (which operated against Cuba)
KMFLUSH: Nicaragua
KMPAJAMA: Mexico
KMPLEBE: Peru
LCPANGS: Costa Rica
LIONIZER: Guatemalan refugee group in Mexico
PBPRIME: the United States of America
PBRUMEN: Cuba
SARANAC: Training site in Nicaragua
SCRANTON: Training base for radio operators near Nicaragua.
WSBURNT: Guatemala
WSHOOFS: Honduras

Other

BGGYPSY: Communist
ESCOBILLA: Guatemalan national
ESMERALDITE: labor informant affiliated with AFL-sponsored labor movement
ESSENCE: Guatemalan anti-Communist leader
FJHOPEFUL: military base
LCFLUTTER: Polygraph, sometimes supplanted by truth drugs: Sodium Amytal (amobarbital), Sodium Pentothal (thiopental), and Seconal (secobarbital) to induce regression in the subject.
LIENVOY: Wiretap or Intercept Program
RYBAT: Indicates that the information is very sensitive
SLINC: Telegram indicator for PBSUCCESS Headquarters in Florida.