CIA

Set to 72 different clues across 90 published puzzles, most often “Spy org.” — The New York Times, Monday, 9 April 2007.

3 letters

Every clue on record, most used first

Spy org.4 times
The New York Times — Monday, 9 April 2007
Tom Clancy subj.4 times
The New York Times — Sunday, 12 June 2005
Cloak-and-dagger org.3 times
The New York Times — Monday, 3 December 2001
"The Company"3 times
The New York Times — Tuesday, 5 July 1994
Org. in "The Bourne Identity"2 times
The New York Times — Monday, 4 January 2010
Secretive org.2 times
The New York Times — Tuesday, 17 July 2007
Subj. of many conspiracy theories2 times
The New York Times — Sunday, 24 June 2007
Kind of operation2 times
The New York Times — Sunday, 27 August 2006
It has moles: Abbr.2 times
The New York Times — Sunday, 31 July 2005
The Company2 times
The New York Times — Thursday, 26 July 2001
Spy's org.2 times
The New York Times — Tuesday, 9 May 2000
O.S.S. successor2 times
The New York Times — Wednesday, 4 December 1996