- Esoteric Happy Ending: Kirk, who earlier had admitted a grudging respect for Khan's methods, respectfully sends Khan and his underlings to live on a nearby planet rather than turn them into authorities. McGivers agrees to go with them. Good to know she and Khan can further their abusive relationship down there! Plus, who's to say they won't find new communities down there to conquer? Of course, this is all moot by the time of The Wrath Of Khan.
- Fair for Its Day: The official reason for the 2013 movie casting the white Benedict Cumberbatch to play him instead of an Indian actor was that the producers would have felt uncomfortable having a man of color as a villain, particularly since that version played Khan up as a terrorist. As others have pointed out, however, they actually didn't get it right in the original series either, as the Indian Sikh Khan was played by the Mexican-born Ricardo Montalban. But in 1967, casting a dark-skinned actor as a dark-skinned character was pretty progressive (remember, this was the same era that gave us Alec Guinness and Anthony Quinn as Arabs and John Wayne as Genghis Khan). And Khan wasn't just a villain, mind you: he was an incredibly brilliant, charismatic world leader who was genetically bred to be superior to other humans in every conceivable way—all of which was unthinkable for a character of color at the time. The Sikh community loved the character for those aspects, and were upset when the film producers threw away the chance for a Sikh actor to play him.
- "Funny Aneurysm" Moment: Spock delivers the ending valedictory: "It would be interesting, Captain, to return to that world in 100 years and learn what crop had sprung from the seed you planted today." Try only about 20 years to find that Captain Kirk's irregular action of marooning the Botany Bay crew in this episode indirectly causes yours and many other's deaths at the hands of Khan, Spock.
- Harsher in Hindsight: The episode ends with Kirk delivering a very optimistic line about the future of Khan's people...
- Hilarious in Hindsight: Kirk, Bones and Scotty explaining to Spock that they can appreciate someone's methods and be against other aspects of their personality at the same time. It's funny because we essentially have a scene explaining "problematic faves" in 1967, over four decades before Tumblr existed!
- Narm: Khan vs Kirk. The Obvious Stunt Double (make that very obvious) and Kirk knocking down Khan with this little plastic thing. Really entertaining.Khan: I have five times your strength. You're no match for me.
[Gets knocked down by a plastic pipe.]
- Values Dissonance: Better awareness of abusive relationships means that McGivers being enchanted, then tactlessly manipulated, by Khan, only looks even more disturbing nowadays. As is Khan and the other Augments being Easily Forgiven by Kirk, though at least that comes back to bite them pretty hard in The Wrath Of Khan.
YMMV / Star Trek S1 E22 "Space Seed"