I find all the silly costumes, sets and props--when compared to TNG/Movie Era and beyond--always gave TOS a somehow goofier, more lighthearted feel. Even when the characters were delving into some pretty deep stuff, by today's standard it can still be seen as a product of its time in both plot points, character development, and set design.
The two darkest TOS eps for me are pretty similar: Dagger of the Mind and Whom Gods Destroy. Both coming from a very different era IRL as far as psychiatric/neuropsychiatric/neurodivergent/etc research has now proven, but in both cases a deeply betrayed trust, fatal consequences, and psychiatric illness is treated as an incurable scourge that can't be managed like other diseases. Seeing the "treatment machine" kill Adams and Garth's cold-blooded dispatch of Marta don't speak well to the efficacy of psychiatric therapies. The story of Gem in "The Empath" is one I am particularly troubled by, for the same reason ("she's nice, she might be nuts, let's kill her!!").
A darker thread that runs through some of my hands-down absolute fave TOS episodes are only mentionable in 2023--I wouldn't hold the writers or producers of the 1960s to these standards, though I do think it would be interesting to see how/if the character treatment would have developed if re-written today. Namely, I'm not the least surprised that Mudd's women tried to flirt their way out of marrying miners, or that Elaan was furious at being shipped off to Troyius to marry a blood enemy: today we'd call that Starfleet's tacit condonement of [human] trafficking. TNG and ENT did touch on some similar themes through their runs, YMMV.
Similarly, I don't know if this counts as dark
per se, but in the same vein, I love everything about Joanne Linville's Romulan Commander in The Enterprise Incident with one glaring exception: you mean to tell me a trained, tested, experienced battlegroup commander in charge of a three-ship patrol in contested space...was just
so bowled over by Spock's galacto-mojo that she tossed all common sense away for a pointy-eared kiss? Maybe it's not dark, but doubtful. Again, not trying to create a space-time rip in morality and hold writers from nearly 60 years ago accountable to today's expectations, as it was
very progressive for its time. But I digress.
Finally: Arena. No reason. I just plain old don't like the Gorn, they give me the creeps. In everything I've seen of them in later series, they don't get any more loveable. Any kind of spooky, eerie, violent, Jurassic-Park-in-Space =
dark to me.