The origin of the name for the JK flip-flop is detailed by P. L. Lindley, a JPL engineer, in a letter to EDN, an electronics newsletter. The letter is dated June 13, 1968, and was published in the August edition of the newsletter. In the letter, Mr. Lindley explains that he heard the story of the JK flip-flop from Dr. Eldred Nelson, who is responsible for coining the term while working at Hughes Aircraft.
Flip-flops in use at Hughes at the time were all of the type that came to be known as J-K. In designing a logical system, Dr. Nelson assigned letters to flip-flop inputs as follows: #1: A & B, #2: C & D, #3: E & F, #4: G & H, #5: J & K. Given the size of the system that he was working on, Dr. Nelson realized that he was going to run out of letters, so he decided to use J and K as the set and reset input of each flip-flop in his system (using subscripts or somesuch to distinguish the flip-flops), since J and K were "nice, innocuous letters."
Dr. Montgomery Phister, Jr., an engineer under Dr. Nelson at Hughes, picked up the idea that J and K were the set and reset input for a "Hughes type" of flip-flop, which he then termed "J-K flip-flops," a name that he carried with him when he left for Scientific Data Systems in Santa Monica.