In the eighth Light Novel of Haruhi Suzumiya, Haruhi tries to get the last page of Kyon's short story because she wants to know the aftermath of the date. He unconsciously touches his blazer, and Haruhi, being the Genre Savvy girl, immediately works out where he hid it and wrestles him to the floor, in this position. Followed soon after by this position. Guess what came to Mikuru's mind when she walks in on this. You're right.
In Jasper Fforde's The Fourth Bear, the MP Sherman Bartholomew built his reputation on being the first openly gay Member of Parliament, but is secretly straight. His husband is aware of his dalliances with women, and has agreed to support him if any of them were to become public knowledge. The same book also featured talking bears who developed addictions to honey and porridge, which were therefore controlled substances.
Parallels are drawn between magic and nuclear power: borne out the structure of the universe, it's immensely powerful and can be employed for much benefit but has to be handled with great care. Places where it went wrong are left barren and toxic and may simply be craters, the waste products are dangerous for centuries afterwards, but it's perfectly safe right up until the moment when it very much isn't. (Terry Pratchett was once a press officer for Britain's nuclear energy providers.)
The prejudice shown by traditionalist dwarfs to those who admit to being female is portrayed in a way that reflects reactionary attitudes to feminism, homosexuality, and transsexuality.
In Thud!, on the other hand, the clash of ideals between moderate and extremist dwarven factions closely resembles similar conflicts in the history of religion, Islam being the most prominent one in recent times. The Fifth Elephant makes the point in the same Dwarvish context that "conservative" does not necessarily mean "extremist".
Jingo was centered around a conflict between the Westernized Ankh-Morpork and the Arabia-metaphor country of Klatch. Anti-Klatchian prejudice bore a remarkable similarity to the xenophobic ignorance shown against Middle Eastern peoples, and the illogic of this stance is lampooned many, many times. (However, the prejudices were less about the modern religious terrorists angle, but about the old British colonial stereotypes.)
In Guards! Guards!, drunk Vimes says (paraphrased): "Ah, life... it grabs you... kicks you in the... in the... y'know, thingies... that you have in the mouth... Teeth. That's it."
Angua wears a leather collar as a part of her everyday clothing and calls her boyfriend "master" (albeit not to his face). She's a werewolf, and has a mild case of dog-like instincts towards humans.
In the Dragaera novels, the Teckla rebellion is clearly reminiscent of a communist revolution. In fact, in one book, a ridiculously long-lived character actually seems familiar with Marx's text and makes this comparison.
Dune's whole "desert planet where everybody speaks Arabic with the most important substance in the galaxy" thing.
The werewolf Fenrir Greyback seems to have some pretty heavy "sexual predator" undertones, what with all his salivating over young children and whatnot. For that matter, the third book's treatment of lycanthropy in general seems to take many cues from the historical treatment of AIDS; at the end of Prisoner of Azkaban, Lupin decides to quit his teaching job when the school finds out that he's a werewolf, knowing that the students' parents wouldn't trust "someone like him" with their children.
A meta-example: Peter Harris' disguised himself in Aunt Dimity and the Deep Blue Sea as a dark haired young man with glasses named "Harry Peters" to avoid hordes of reporters after his grandfather wrote a letter to The Times bragging about him. Hmm, a dark haired young man with glasses plagued by fame...
Lori is struck by waves of déjà vu when she goes to Bluebird, Colorado: many of the locals closely resemble her neighbours in Finch, down to similar-sounding names.
At the close of one of their conversations on Mistress Meg Redfern in Aunt Dimity and the Village Witch:
You've grown fond of Mistress Meg, haven't you? "Yes, I have," I said. I can understand why. She was independent, bullheaded, energetic...Hmmm...Who does she remind me of? "Goodnight, Dimity," I said with a wry smile. Good night, my dear.
In John Green's An Abundance of Katherines, Lindsey has a cave. It seems like more of a short tunnel. She's never had anyone else in there, but she wants the protagonist to go in. She remarks that it's a bit tight, but she'll guide him in. She also notes that she must have overlooked that opening a hundred times before noticing something special around eighth grade, when she started using it whenever she was having "me time".
In John H. Ritter's Choosing Up Sides, 13-years-old Luke's left-handedness is treated in the same manner as homosexuality. His father has always tried to correct his tendencies, for fear he'll go to Hell, and Luke believes for a while that he can change if he tries hard enough. His uncle even tells him there's no point in trying; he's simply "oriented that way".
There was SF short story in which people would regularly have sex in public, pay for sex, and treat sex as a generally essential part of life... but ate in private and were ashamed if anyone found out they'd paid someone to cook for them.
Anything and everything that happens or is discussed in Invisible Man has something to do with race relations, from the ingredients in the paint the main character helps to make, to the cast-iron bank he keeps trying to get rid of. It gets more than a little Anvilicious at times.
In Lord of the Flies, there is a scene with a mother pig, whom the boys force away from her piglets, and then spear. This is reminiscent of some soldiers gang-raping a mother. A few quotes, in chronological order:
The spear moved forward inch by inch and the terrified squealing became a high-pitched scream.
Then Jack grabbed Maurice and rubbed the stuff all over his cheeks.
"Right up her ass!" [One of the boys is bragging about where he managed to get his spear.]
The eternal rivalry between the Summer and Winter courts of the faeries bears more than a passing resemblance to the Cold War between America and Russia. Both sides are pretty much equal in strength, and it's clear that a full scale conflict between them would, in the most likely scenario, largely wipe both sides out and send the world into a new ice age, but if it looks like one side's showing weakness ... well, they just have to exploit it. That's what archenemies do, right?
In Grave Peril, Harry is captured by the Red Court and, while he doesn't go into detail about what they do to him, Bianca's straddling him and shifting from beautiful, seductive woman to monstrous vampire, the way the Red Court finds feeding to be a key turn on, in a dark variant of Erotic Eating, and his statement "They did things to me," subtly plays up the gang rape angle. And, when he appears a few months later in Summer Knight, while he's grim, anti-social and short-tempered partly because he's spent his time trying to cure Susan and failing, it's not unreasonable to suggest that part of it is his reaction to what they did to him.
A lampshaded, in-universe example occurs in Ghost Story. Ghost!Harry, being incorporeal, tries to possess Molly's body and channel magic through it. She fights this initially, trying to push him out, but relaxes after he tells her his identity and lets him go inside her. She notes how suggestive it was later.
In The Heroes of Olympus there is an amnesiac hero with a ton of martial skills and esoteric knowledge named Jason.
In The Witcher novels the presence of the Witchers can be sensed as a tingling sensation by sensitive people. There's a reason why they all seem to attract the opposite sex quite a bit. Likewise, in The Blood of the Elves a 13-year old girl learning to be a sorceress draws power from the earth, an experience that's described in a manner reminiscent of menstrual cramps and concluding in an orgasm.
Roald Dahl's The Witches includes a scene where the protagonist is dragged out of hiding by a group of witches and force-fed a potion as they hold him down.
Orion Pax listened, and cataloged, and archived, and indexed, but his mind was not on his work... Who was this Megatron, this gladiator thug, killer of criminals and criminal himself, who gave voice to a longing that Orion Pax had never known he felt?
Goblin Market is full of this trope, sometimes disturbingly so, with multiple scenes that suggest a connection between the consumption of food and seduction or attempted rape.
In The Berenstain Bears and the Sleepover, the Sleepover that Sister Bear is attending ends up going way out of control to the extent that the police arrive shortly thereafter and the parents take the children home to punish them, and then they have to clean up the mess. Gee, that sounds like something from a stereotypical Party House from one of those high school films like Superbad.
The Butter Battle Book concerns two peoples split by a trivial ideological difference (which side toast should be buttered on), locked in an arms race that escalates to the point that if either side actually acts, both will be destroyed. If this sounds exactly like the Cold War as seen by its detractors, congratulations, you just got the point of the book.
The Sneetches is this trope about racism. There are Star-belly Sneetches and Star-less Sneetches, and the Star-Belly Sneetches have cookouts and picnics that the Star-less Sneetches are excluded from and generally look down on the Sneetches without stars. Then a Snake Oil Salesman shows up with a way to give the Star-less Sneetches stars, and when the Star-Bellies get incensed at the inability to tell the difference, said salesman gives them an opportunity to remove their stars and the "hierarchy" switches, and then all of the Sneetches end up removing and regaining their stars until none of them have any more money to pay the salesman...only to decide that since no one was quite sure who was who, they might as well forget about this whole prejudice thing and live together.
DH Lawrence's Women in Love has Gerald Crich, the typical manly man. In one of the scenes, he's shown riding a horse, and a train comes by. The horse is naturally afraid of the noise, but Gerald holds her there and forces her to endure it. The way it's written makes it sound like a rape scene, and it's very unsettling.
New Moon has young men literally exploding out of their clothes when they turn into animals. Predatory animals.
Eclipse has two instances of one of those young men "showing his love" by forcing himself on a girl, just in case we didn't get it the first time.
In The Penderwicks,Jeffrey's only friends (as far as we know) are the eponymous quartet of Penderwick sisters and he is revealed to have a talent for playing music. However, his overbearing mother wants him to go to a military school to follow in his father's footsteps. Hmmm...
Used In-Universe in The Forbidden Game. After an accident at her Grandfather's house when she was five, Jenny was covered in scratches, her clothes were torn and she refused to talk to anyone. Jenny's friends had been under the assumption that her Grandfather had hurt her before disappearing, but after confronting her memory in the game they eventually find out it was the Shadow Men.
I Robot: In Little Lost Robot a scientist at US Robots, Dr. Bogert, repeatedly calls robots "Boy". And the story Runaround the robots stationed at Venus must call all humans "Master":
In Right Ho, Jeeves Berthie relates Jeeves the descent and fall of Augustus Fink-Nottle, from Newts as a harmless hobby to a dark obsession:
Bertie: ... Well, Gussie has always been a slave to them. He used to keep them at school. Jeeves: I believe young gentlemen frequently do, sir. Bertie: He kept them in his study in a kind of glass-tank arrangement, and pretty niffy the whole thing was, I recall. I suppose one ought to have been able to see what the end would be even then, but you know what boys are. Careless, heedless, busy about our own affairs, we scarcely gave this kink in Gussie's character a thought. We may have exchanged an occasional remark about it taking all sorts to make a world, but nothing more. You can guess the sequel. The trouble spread, Jeeves: Indeed, sir? Bertie: Absolutely, Jeeves. The craving grew upon him. The newts got him. Arrived at man's estate, he retired to the depths of the country and gave his life up to these dumb chums. I suppose he used to tell himself that he could take them or leave them alone, and then found—too late—that he couldn't. Jeeves: It is often the way, sir.
The whole plotline about Stacey's diabetes and the associated stigma leading to her moving away from New York lest she lose all her friends. In retrospect, the series' origins in the late eighties makes it likely the diabetes stood in for HIV (considering very few people lose their friends over having diabetes).
It's mentioned constantly that Mary Anne's father loosened up considerably when he started seeing Dawn's mother. Adults rereading the series might read between the lines a bit.
In The Amazing Days of Abby Hayes, Laurie, a very stringent Granola Girl, finds chocolate in her five-year-old daughter's sleeping bag that Abby gave to her and immediately becomes very angry with her. The scene is played out as if the chocolate was an illegal drug of some sort. Which, from Laurie's point of view, it is.
Abby:[writing in her diary] She said I had betrayed an innocent child's trust. She said Wynter would bear lifelong scars. She made it sound like I had committed an awful crime.
Glen Cook's Water Sleeps is meant to be reminiscent of The Vietnam War. A small force fights a guerrilla war against a numerically superior army with a powerful entity at its head, with the distinct impression that said entity doesn't care much about the health of the country it's occupying. The local powers regret letting her in in the first place, but have no way of getting rid of her. All of this happens on a backdrop of jungle and city. If that doesn't do it for you, the monk who immolates himself in front of the seat of government early in the story will.
In City of Fallen Angels , Simon says that Kyle grows weird plants on his balcony. He then follows it up by claiming they aren't drugs. The plants turn out to be wolfsbane.
In-universe, at the end of The Diamond of Darkhold, where Doon has to once again has to put together some letters with Lina that have been broken apart by deciphering the phrases. It sparks off their Maybe Ever After.
Ignore the context of this conversation from Vampire Academy and all the background knowledge you have of the characters for a moment and read this. Sounds as lovers confronting each other.:
“Why didn’t you tell me?” She cried. “I couldn’t tell anyone,” I said. “You should have told me,” She repeated, “I feel like you don’t trust me.” “Of course I trust you.” “Is that why you’re sneaking off?” “That has nothing to do with trust,” I admitted, “It’s me... well, I didn’t want to tell you. I couldn’t bear to tell you I was leaving or explain why.”
Star Wars: Shatterpoint is a very thinly veiled allegory for European imperialism, mish-mashing various elements from the colonisation of African and South and South East Asian nations (the off-worlders come to Haruun Kal to harvest and export the valuable rare spices and other plants) and the genocide of Indigenous peoples (the Korunnai and their herds are shot on sight by civilians and militia alike). The whole planet could easily be considered a ramshackle African nation if set on Earth. There's also more than a few parallels with The Vietnam War, what with invaders with superior technology fighting a protracted war with no end in sight against local guerrilla fighters who use the jungle itself as a weapon. Once Mace Windu arrives and sets the planet straight with the help of the Republic army, he declares the whole mess a "police action" rather than a war, a phrase which instantly brings The Korean War to mind. Windu's reasoning is sound, however; if not for bribery and corruption, the Republic law enforcement would have nipped the problems in the bud long ago.
Red Moon Rising, hoo boy. The basic treatment of wulves is quite similar to that of racial minorities in the modern world. The kennels are seen as internment camps by wulves and wulf-sympathizers, which isn't too far off since there were actual internment camps for wulves during WWII. The Change and stigma associated with it rings similarly to mental illness. Danny telling his mom about his wulf side surfacing is a lot like a Coming-Out Story, complete with him being temporarily kicked out.
In The Hunger Games, in District 11, the dark-skinned population is forced to farm and are treated with particular brutality. This sounds a lot like slavery in the American South. Panem and District 13 are nuclear powers locked in a stalemate. Panem is decadent, wealthy, and corrupt. Its citizens enjoy outrageous luxury while they exploit the surrounding communities to feed their enormous appetites. District 13, on the other hand, is a dull and drab place, ruled by an at least equally totalitarian regime that regiments every aspect of its citizens' lives. That's how the US and the USSR portrayed each other during the Cold War.
In the real world, critics have noted many similarities between the basic concept of the trilogy and a Japanese novel, manga series and film entitled Battle Royale, which also dealt with children being forced by the government to fight to the death, with the same use of allegiances, supposedly doomed lovers facing the moment they might need to kill each other, the revelation that even children can become psychopathic murderers, and a rebellion movement of sorts.