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."
"Whistling in the Dark" is a common idiom meaning “to put on a brave front.”
"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."
"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).
"Squeaky Floorboard, Sudden Death" appears to be a Splinter Cell reference, in particular to the third game in the series, Splinter Cell: Chaos Theory.
"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.
"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'."
"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.