The following is based on unverified behind the scenes information and has not been confirmed by canon sources.
The entire collection of manuals may be based on the "Department of the Army Field Manual."
U.S. Covert Operations Manual - Whistling in the Dark might be a reference to the Splinter Cell series where the player can whistle to lead enemy guards to their location.
U.S. Covert Operations Manual - Not the Soldiers You're Looking For is a reference to Star Wars: Episode IV: A New Hope, where Obi-Wan Kenobi says "These aren't the droids you're looking for."
U.S. Covert Operations Manual - Who Goes There? is the name of a science fiction novella by John W. Campbell, Jr., written in 1938 and made into several films, the best known of which is John Carpenter's The Thing (1982).
U.S. Covert Operations Manual - Squeaky Floorboard, Sudden Death appears to be another Splinter Cell reference, in particular to the third game in the series, Splinter Cell: Chaos Theory.
U.S. Covert Operations Manual - Bushes, Boxes and Beehives Camouflage Special could be a reference to the Metal Gear Solid game series, of which hiding in a cardboard box is a signature, and where Snake may hide behind bushes, under boxes and use beehives as a method of distraction.
U.S. Covert Operations Manual - Look better in black is possibly a reference to a quote from City of Bones, part of the Mortal Instruments series of novels. The quote is as follows: “It means 'Shadowhunters: Looking Better in Black Than the Widows of our Enemies Since 1234'.”
U.S. Covert Operations Manual - Tiptoe Through the Tulips is a reference to the song "Tiptoe Through The Tulips" by Nick Lucas, from Gold Diggers of Broadway.
End of information based on unverified behind the scenes information.