After watching the second (and series-winning) pilot, Where No Man Has Gone Before, the theme of Supermen and Gods just clobbered me over the head. Gary Mitchell (and Dr. Elizabeth Dehner) in that one of course. Then there is Khan Noonien Singh in Space Seed, Apollo in Who Mourns for Adonais, and Sargon's race in Tomorrow is Yesterday. I'm not talking about mere dictators nor special powers. Those are other themes. But Roddenberry obviously had a thing about men approaching godhood and/or the equivalent, gods being merely mortal. Notice that in each instance, the superman/god must be brought down by the end of the episode. Time to scan the episodes again and see if I missed any additional instances of this theme... I find no other direct instances. A weaker related theme does appear however: being (falsely) worshiped as a god. Apollo, in the past, is an instance of this. But there are several episodes depicting ongoing worship, the most representative episode being The Apple in which Vaal is worshipped. Of course in all instances the erroneous worship must be corrected somehow. The other instances I find are: The Paradise Syndrome in which Kirk is worshipped as the god Kirok, For the World is Hollow and I Have Touched the Sky in which The Oracle is worshipped, Bread and Circuses in which the slaves worship the sun/son (note: this is a special case), and And the Children Shall Lead in which Gorgan is worshipped by the children. The criterion "as a god" gets more tenuous however, which leads to a further list of episodes where there is a weaker version of the same dynamic, i.e. reverence rather than worship -- of Cochrane by The Companion in Metamorphosis, of the Holy Words in The Omega Glory, of The Book in A Piece of the Action, and maybe even of Gill in Patterns of Force, although I think we've crossed the line into "mere dictators" there. On an opposite tack, there are a couple of episodes where a feared entity is referenced as devilish -- the Horta in Devil in the Dark of course, but also the Doomsday Machine which Decker at one point describes as "straight out of Hell". And finally there are the mere references to the Bible or to gods which one might find in any series -- Whom Gods Destroy, The Way to Eden, Requiem for Methuselah, even the "delusions of godhood" reference in The Trouble With Tribbles and the "laws of God and men" in The Ultimate Computer.
Before moving on to dictators and special powers, I want to cover the even more dominant theme of Insanity. I don't know if Roddenberry had some special connection to or interest in mental health, or whether it was just a convenient route to increased drama. But there are a full two episodes set in mental asylums, and many additional characters depicted as literally insane. The episodes are of course Dagger of the Mind and Whom Gods Destroy. The individual characters are: Lenore Karidian in The Conscience of the King, Ben Finney in Court Martial, Lazarus in The Alternative Factor, Matt Decker in The Doomsday Machine, Richard Daystrom in The Ultimate Computer, Larry Marvick in Is There in Truth No Beauty?, Dr. Sevrin in The Way to Eden, and Janet Lester in Turnabout Intruder. There are several additional examples of temporary insanity: everyone in The Naked Time, McCoy in City, Spock in All Our Yesterdays. And if we relax to the milder mental abberations of obsession and the like: Kirk in Obsession and in A Private Little War.