These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Complete Monster: The Un-Man, who is heavily implied, if not outright stated to be Satan. He is a source of all evil, trying to corrupt Perelandra in order to lead it to destruction. While he isn't "working", he tortures to the brink of death without killing.
Also in Perelandra the underground section can be incredibly creepy. Not just because most of it takes place in total darkness, but because there are lots of hints that all sorts of bizarre persons and places exist down there and the reader only sees enough of them to hint at it. And what little we see is hinted to be not necessarily evil but so foreign to human experience that it's incomprehensible.
The detailed description of the head and the creepy paintings in That Hideous Strength. Also Dr. Frost's POV segments.
Older Than They Think: That Hideous Strength addresses the issue of transhumanism and many of its implications. Its first printing was in 1945.
Seinfeld Is Unfunny: At the time the trilogy was first published, most aliens in SF stories were hostile savages intent on destroying humanity. For Lewis's aliens to be morally superior to man was a radical departure... which was widely adopted by later writers, somewhat diluting its impact today. Though the thing that remains the most original with Lewis' premise is that his aliens still believe in a deity, while most other sci-fi examples don't.
Values Dissonance: You're in a theological debate. You find yourself losing the argument and fear that your audience might be swayed towards the opinions of your opponent. What do you do? If you're Ransom, you follow the advice of a "divine voice" and simply kill the bastard. The intended message is supposed to be an anti-appeasement one (the book was published in 1943): sometimes it's not enough to be right - some people can't be reasoned with, and for the good of all you have to use force. However, in the context of the story where his opponent is playing by the rules and technically isn't harming anyone (he's convincing them to do it themselves), it accidentally comes more across like, "If you're losing an argument, just beat the crap out of your opponent because you know you're right."
There are, however, mitigating factors:
This wasn't just a debate between two people with equally valid points. It was literally the devil incarnate, trying to convince another world's Eve to disobey God and duplicate the fall of man, thereby wrecking another paradisal world For the Evulz. Ransom's task was to prevent this from happening by any means necessary.
This was his last resort. He came to this conclusion only after being dragged through weeks of argument.
Ransom was physically and mentally exhausted because the Un-Man, being demon-possessed, did not need to sleep. He abused this by engaging Tinidrel when Ransom could no longer stay awake, or by deliberately keeping Ransom sleep-deprived, to the detriment of his mental health.
It required tremendous courage on Ransom's part. He was certain that physically battling the devil would mean his death. Fortunately for him, the body the devil was inhabiting belonged to another out-of-shape professor.