This is all subjective and really "your 10 least favorite episodes." I don't think I really hate any of them. However, some episode are a chore for me to sit through, even if there are things about them individually that I enjoy.
Charlie X: the singing, the painful ass slapping antics and Kirk in tights. They should have smacked Charlie shitless "when I came aboard!"
Miri: No blah blah blah. Kirk creepily comes onto Miri from minute one.
Mudd's Women: the sleazy music, the ass ogling and Roger C. Carmel. No thanks.
I, Mudd: Roger C. Carmel. The over the top humor. The evacuated invisible crew. I am not programmed to respond in that area.
The Apple: Chekov constantly macking on Yeoman Landon, the planet of blonde people who laugh at kissing, the virtual replay of the ending of Who Mourns of Adonias and Mallory, who was trying not to be noticed, screaming his bloody head off before stepping on the exploding rock.
Patterns of Force: "Hitler made the trains run on time, so let's pattern a government after the Nazi's." The most misguided Trek ever.
A Piece of the Action: okay, I do hate one episode and this is it. Only a single funny line in the whole episode (Spock: "I'd advise yez ta keep dialin', Oxmyx"). Anything with Vic Tayback is bound to be obnoxious.
And the Children Shall Lead: the circle jerking kids, the fat phantom, Uhura's mirror at her station and Sulu's fear of Space Knives. What's to like?
Mark of Gideon: WTF? That is all.
The Way to Eden: actually treats young people as badly as Miri. And when did Chekov become such a tight ass? "His name was Adam." Thanks for hammering that home Spock.
Runner up: This Side of Paradise, merely for the painfully bad Jill Ireland. The only thing I ever saw her in that I liked was the Man from Uncle episode where she played a stripper. She had a HELL of a figure.