The Lion, the Witch, and the Wardrobe: Lewis himself explained that the first book of what is now The Chronicles of Narnia was initially written as a stand alone piece revolving entirely around the image of a faun carrying a pile of packages and an umbrella, in the snowy woods, next to a lamppost. The symbolism of Aslan as Jesus was entirely accidental. He attributed it to his values subconsciously coming out. It wasn't until this similarity was pointed out to him by fans and critics that he started purposely writing that way; he saw writing as way to spread the Gospel. This is why, in a study of the Chronicles in their entirety, this book has some of the weakest symbolism and allegory, much more akin to Tolkien's "applicability" in the Lord of the Rings. (It also explains why Wardrobe was Tolkien's personal favorite of the Narnia books; he found them increasingly insufferable as they became more suppositional.)
A lot of his nonfiction: While his religious books have always been his most popular, Lewis wrote quite a bit of literary criticism and history too.
Till We Have Faces: While the Christian themes are there, they're pretty subtle and easy to miss if you're not looking for them. It is a retelling of a pagan myth, after all.
A Very British Christmas: In a very humorous piece in God In The Dock,Herodotus visits the island of Niatirb and concludes that the resident barbarians observe two entirely separate holidays on 25 December: Exmas (a commercial racket) and Crissmas (a religious festival). Also, Father Christmas shows up in Narnia.
Big Creepy-Crawlies: In Surprised by Joy, Lewis writes that his nightmares during childhood were either about ghosts or insects. Of the two, he found the dreams about insects much more frightening.
In The Pilgrim's Regress, young John is told that the damned are tortured by scorpions the size of lobsters.
In Perelandra, Ransom encounters flies and beetles larger than himself in the caverns of Venus. Subverted in this case. Once the Un-man's presence is gone, Ransom ceases to find them frightening, and speculates that they may, in fact, be sentient.
In The Problem of Pain he discusses the moral problem of the suffering of animals(who after all are not either being punished for something or being trained in how to be good and therefore not subject to some of the possible explanations for human suffering). In fact he does take the question seriously. But when he gets to discussing animals and the afterlife, he imagines someone asking "Where do you put all the mosquitos" and then notes ironically that heaven for mosquitos and hell for humans might be "very conveniently combined."
Boarding School of Horrors: Lewis had an extremely unpleasant experience at school, compounded by the fact that his first teacher was a literalSadist Teacher to the level of actual clinical insanity. Not surprisingly, boarding schools in Lewis's works are very unlikely to be positively portrayed.
Another school he went to had an overweening "aristocracy" of Jerk Jocks supported by teachers which engaged in organized bullying and even rumored pedophilia toward the underclass students. (The second of which Lewis actually said was, under the circumstances actually a saving grace because it got their minds off their snobbishness!) Lewis hated that school so much that he almost considered World War One less unpleasant: no one said you had to pretend to like it, after all.
In general, C. S. Lewis's father was not good at picking boarding schools.
Combat by Champion: Prince Caspian features a particularly gut-churning edge-of-your-seat example. All the more so for Peter's quiet dignity.
For the Evulz: Deconstructed in Mere Christianity: Although it is possible to do good for the sake of doing good, nobody does evil for the sake of doing evil; evil deeds are merely the pursuit of good in the wrong way.
Humans Are the Real Monsters: Appears to some extent in practically all his work, but his non-fiction dedicates entire chapters to expounding on how and why humans are bastards, and how the bastardliness can be reduced.
In one of his essay's, he mentions Dark-Gods-of-the-Blood which comes down to how we must always fight off the desire to give into the baser desires we feel as we go through daily life.
It's All About Me: A theme of many of his theological works, especially The Great Divorce. Lewis views Pride as the cardinal sin, and the source of all other sin.
You must picture me all alone in that room in Magdalen, night after night, feeling, whenever my mind lifted even for a second from my work, the steady, unrelenting approach of Him whom I so earnestly desired not to meet. That which I greatly feared had at last come upon me. In the Trinity Term of 1929 I gave in, and admitted that God was God, and knelt and prayed: perhaps, that night, the most dejected and reluctant convert in all of England.
Viewers Are Geniuses: His work geared at adults is often peppered with untranslated Latin or French phrases, under the assumption that his readers will know what they mean.
Likely enough at the time when large numbers of upper and middle class English would have learned those at school.
What Could Have Been: A scholarly book entitled Language and Human Nature was begun but never completed. The rub: It was to have been coauthored with J. R. R. Tolkien. . Mind you, he fought in a World War, so we should really be thankful we had him at all....
World War II: Much of Lewis's fiction (The Screwtape Letters, The Great Divorce, five of the seven The Chronicles of Narnia books, and the second book in The Space Trilogy, specifically) takes place during the War. It's usually not dealt with extensively, but you can catch plenty of references to the Blitz and the subsequent air raids, blackouts, etc. all the same. This is understandable, as Lewis lived in England and did much of his writing during the '30s and '40s.
What later became Mere Christianity was originally a series of wartime radio broadcasts given by Lewis, meant to lift the spirits of the British people. These broadcasts were only edited and put into print after the war was over.