The change in Gary and Elizabeth's eyes was accomplished by Gary Lockwood and Sally Kellerman wearing sparkly contact lenses. They consisted of tinfoil sandwiched between two lenses which covered the entire eye. Wearing the lenses was difficult for Lockwood. He could only see through the lenses by looking down while pointing his head up. Lockwood was able to use this look to convey Mitchell's arrogant attitude.
During filming, the studio was infested with wasps who had built a nest up in the rafters. Sally Kellerman and William Shatner were both stung, the latter on his eyelid which swelled up, causing delays in the filming of some of his scenes.
According to the Starfleet Access commentary on the Blu-Ray, the remastering crew debated over whether or not to change the middle initial on the "James R. Kirk" tombstone to the proper T. While some members of the crew were for it and some against it, they ultimately decided not to, due to the ridiculous amount of rotoscope work it would have required.
The familiar colors and positions of the crew had not yet been finalized when this second pilot was shot. The tunics for operations crew are beige instead of red. The locations of the helmsman and navigator are reversed (when Kirk is facing the viewscreen, Mitchell, whom Kirk addresses as "helmsman," is on his right, and Kelso, the navigator, is on his left). Spock is wearing a gold command shirt, not a blue sciences one. Both Mitchell and Kelso wear beige operations shirts, rather than the gold command shirts later associated with their stations. Smith, the captain's yeoman, wears a gold command shirt, and Lieutenant Alden, the communications officer, wears a blue sciences shirt, rather than the operations shirts most later yeomen and communications officers would wear.
Arlene Martel was originally considered for the role of Dr. Elizabeth Dehner But Martel has sensitive eyes and there was concern that the silver contact lenses that the role required would have caused damage to them. She later guest starred in Star Trek: Amok Time (1967).
While the bridge of the Enterprise appears similar, the main viewing screen is very different having a larger border, rounded corners and a narrower aspect ratio more like television at the time of shooting.
The gap in time between filming this and the rest of the series explains some of the apparent inconsistencies, notably some changes in the Enterprise architecture, the fact that most of the female crewmembers wear trousers and Mr Spock's peculiar yellowish skin tone.
According to the tombstone that the "godly" Gary Mitchell creates for Captain Kirk, we see that Kirk was born on Stardate 1277.4. Of course this information is widely debatable, given the numerous inconsistencies with the first few episodes of this series (such as Kirk's name being James R. Kirk, which later becomes T, etc.).
During the opening scene while Kirk and Spock are having a chess match, Spock acknowledges his mixed blood but attributes it to an ancestor in his lineage which in subsequent episodes it was later developed that he was the offspring of a Vulcan male and a human female.
Both pilots for Star Trek (1966) - Star Trek: The Cage (1986) and "Where No Man Has Gone Before" - were the only episodes not filmed at the current-day Paramount Studio lot in Hollywood. They were filmed at the present-day Sony Pictures Culver Studios in Culver City, California.
The photo images of Dr. Dehner's and LCDR Mitchell's medical records reveal part of their home addresses on Earth. Dehner was born in a town called Delman; Mitchell in Eldman. The town names are simple anagrams of each other.
The title is based upon the opening credits introduction. "Space - the final frontier. These are the voyages of the starship Enterprise. Its five year mission: to explore strange new worlds, to seek out new life and new civilizations, to boldly go where no man has gone before."