False Camera Effects: Most notably, the first/zeroth episode consists of a simulated student film; but the whole anime has scenes drawn with simulated lens flare, barrel/pincushion distortions and fisheye lenses all over the place.
Fan Disservice: In episode six of season two, Koizumi's swim trunks are swapped with a tiny, black Speedo. Still fanservice to some, though.
Fanservice: Special mention to episode three of season two. It's essentially a repeat of episode two by nature of being part of a "Groundhog Day" Loop, but has gratuitous amounts of fanservice for both guys and girls Specific focus given to Itsuki's and Kyon's bodies during shirtless scenesand an additional shirtless scene for Kyon at the beginning (he was wearing a shirt that time last episode!) as well as to Haruhi's and Mikuru's... assets. Also, close ups to the face play up Itsuki's bishonen-ness and the girls' moe-ness (and the entire episode seems to intentionally defy anyone to resist hugging Yuki). To cap it all, there's some Ship Tease all around for Kyon/<SOS member here>. (Kyon has reactions to each of the girls' aforementioned Moe facial expressions, and even Itsuki arguably has his bit of ship tease). The episode just screams "intentional gratuitous fanservice."
Yuki. Grapples with a combat knife by its blade. Intercepts lasers with her palm. Takes several steel spikes through the chest. Impaled with steel spike the width of a ship's mast and lifted off her feet. Only the latter is enough to make her fall over — and even then, it's from exertion, not pain.
Then, of course, it gets horrifically subverted in Disappearance — Yuki has made herself fully human to finally be with Kyon. Now that she's human, though, she can feel pain and has a natural terror of it... meaning she can't rush to his rescue when Ryoko shows up for round two, as her old crazy stunting would only get her killed in agonizing minutes as a human. It doesn't help that she can't even remember her old stunts due to the way she rewrote the world and herself.This can lead to a little confusion when it looks like she grabs the knife anyway, but later on in the novels we learn a bit more about the rest of the incident and it turns out the actual trope is still in full force.
Female Gaze: Exactly how Tsuruya sizes up Kyon when they meet in The Boredom of Haruhi Suzumiya.
Kyon admits to Haruhi that he has a thing for ponytails, and encourages Yuki to lose the glasses because he isn't a fan of meganekko.
In one of the novels, he admits to himself that Mikuru's maid outfit is his favorite one and wonders if he has a maid fetish.
And later novels he subverts this trope by noting he finds seeing Yuki in her uniform especially comforting, but not because he has a sailor uniform fetish.
Figure It Out Yourself: Both Mikuru Asahina (big) and Yuki Nagato give Kyon very incomplete information about how to ... save the world from Haruhi. Kyon puts both clues together at nearly the last minute to do just so. Justified to some extent because both Asahina and Nagato are constrained by rules. It's actually pretty obvious. Kyon is just selectively oblivious as long as possible.
In the books, "Endless Eight" was a brief story that lasted about 30 or so pages and the time loop was broken without the reader seeing any other repeats after Kyon has Haruhi help him with his homework. In the anime, it's eight episodes of near-identical footage and dialogue, reanimated from scratch every single time (which in turn angered those who viewed the affair as a waste of money and season). You can just skip episodes 3-7 of second season and literally miss nothing.
Although overshadowed by "Endless Eight", the first season episode "Someday in the Rain" had 3 minutes and 23 seconds of continuous filler, with irrelevant chatter going off in the background while Yuki reads, occasionally turning the page. It was interrupted for a couple seconds with a scene of of Kyon riding the train.
Kyon refers to Haruhi by her first name, no honorific extremely soon after the SOS-dan's founding, and she's the only one to call him by just his nickname, no honorific. Also notable is that Yuki never, ever refers to Kyon by name, only "you". Neither does Koizumi.
Also significantly, Haruhi's the only person that Kyon addresses by first name and no honorific.
In the student film, the characters are supposed to refer to each other by first name, but the actors sometimes flub their lines and use last name.
End of the Disappearance movie (not the novel): "I'm sorry, Nagato...Yuki." However, it's unclear if he was using her name or simply pointing out the fact that it had started snowing (or both).
First Time Feeling: In Disappearance, Kyon discovers that Nagato set the whole plot in motion by developing emotions and, unable to deal with them, stole Haruhi's powers and remade the world.
Five-Man Band: Lampshade hanging, Haruhi purposely creates the club to her expected stereotypes. Although, it should be noted that the roles change depending on the point of view. According to Haruhi, she is The Hero, Yuki is The Smart Guy, Koizumi is The Lancer, Kyon The Big Guy, and Mikuru is obviously The Chick. But for Kyon, Yuki is The Big Guy (and to an extent, his Lancer) and Koizumi is The Smart Guy. So Haruhi would probably be Kyon's Lancer or vice versa. (Guess who he calls first when something happens....) He calls Haruhi when a the time-shifted version of Mikuru(Michuru) gets kidnapped. Luckily she thinks it's a joke.
Flashback: For example, after the SOS brigade finishes the movie, we see what happens right after Haruhi meets Kyon at the end of Melancholy Part VI.
Flash Step: Done by Yuki twice to stop Mikuru's eye beams.
Episode 00 has everyone in more or less role they play in the series, Kyon's the Narrator, Yuki's an Alien, Mikuru's a time traveller and Haruhi's the Director so everyone has to bow to her wishes.
Kyon makes an offhand comment in Novel 11 that Koizumi is the last member of the brigade you would want to see angry. And who should be the one to explode (literally) at Fujiwara in the climax?
In one early episode (chronologically, not the broadcast order) Yuki mentions that Haruhi would never believe Kyon if he told her about Yuki being an alien. This is exactly what happens when he finally does decide to tell her at the end of the series
In the third novel/first series story "Remote Island Syndrome," Haruhi notes that it's better to go to an island in the summer, because you can't get caught in a blizzard unless it's the winter, with Kyon even noting that isn't something to hope for. Sure enough, in the fifth novel, they visit the mountains in winter and get caught in a blizzard.
Forgot the Call: There are scenes that indicate that Haruhi is up against a mental block as opposed to just being totally clueless. Note how something stops her in midstream here: "I'm the brigade chief and director and ... Anyway, I won't allow you to go against me!"
Fortune Teller: Yuki in "Live Alive". However, as Kyon points out, she doesn't understand the difference between telling somebody their fortune and predicting their future; for example, she tells someone that he'll drop his ice cream in ten point three minutes.
Freeze-Frame Bonus: In the first part of the two-episode island mystery arc, there's a shot of the sunset, and then a wave passing over the beach. Pause in the two or three frames before the wave crosses the screen, and you'll see a bizarre sketch in the sand of...something. Haruhi? A caveman? Itsuki in a bikini?
Frickin' Laser Beams: For the most part averted; nobody is able to dodge them and they're even invisible! Completely averted if you can believe Yuki can run at faster-than-lightspeed to block them (and she probably can).
Underage drinking is a big no-no to the Japanese (or at least depictions of it are). In the Sigh novel, Mikuru was slipped tequila; the anime changed this to amazake, which is seen as alright to give infants, which makes Mikuru seem much, much worse at holding her liquor (not that she wasn't already bad in the original). In a rare inversion, the English Dub actually changes it to sake.
In Boredom the ''Remote Island Syndrome" segment has the entire cast get very drunk twice (with the possible exception of Yuki). The anime adaptation cuts this out entirely and drags Kyon's little sister along just to make sure everyone stays on their (relative) best behavior.
While Haruhi is talking about how she doesn't see the point in love, there is a brief cut to a random scene outside where a male student helps out a female student with something, and it's all very flirty. Later in the episode, there's another brief cut to where the female student shoves the male student to the ground and runs away.
Multiple in "Live Alive":
Two TV personalities "Hard Gay" and Akihiro Miwa grab Kyon as he's walking through the halls.
When Kyon is leaving the building at the festival, there's a mom getting a balloon for her kid. The kid protests, and the mother threatens to leave the kid behind.
When Kyon goes into the hall so he can doze through a concert (having just been up all night editing the brigade's movie), someone else appears to have already fallen asleep a few rows in front of him.
Achakura, Ryoko's (still psychotic) but barely two-feet-tall incarnation from Haruhi-chan, is notable in that she's tiny compared to the rest of the heavily chibified cast.
Fun with Acronyms: SOS Brigade stands for Sekai wo Ooi ni Moriageru tame no Suzumiya Haruhi no Dan, or Haruhi Suzumiya's gang whose purpose is to greatly enliven the world. To maintain the joke, the fansubbers and the official manga and light novel, gave this as Save the World By Overloading It With Fun — Haruhi Suzumiya's Brigade, while the official dub translated it as Spreading Excitement All Over the World with Haruhi Suzumiya's Brigade.
Future Imperfect: Asahina sometimes does this. For example, she comments on Koizumi's telescope being "not very different from Kepler's." This particular example could actually make sense, who knows how future telescopes work? In Asashina's time they might use non-optical telescopes, or more conventional telescopes built into contact lenses, or even simply direct the visual input into their minds. From this point of view, there is little difference between two cylindrical telescopes with glasses, and only half a millennium's development between them.
Genre Savvy: Haruhi insists on seeing Genre Tropes everywhere, even where they might not have existed; in a completely different way, Itsuki attempts to "appease" Haruhi by providing textbook, predictable examples of tropes. Haruhi does not do "predictable", so these tend to mutate.
Girl in a Box: Kyon's little sister hid in his duffel bag so he would take her on vacation with him. Amusingly, Reality Ensues - Kyon immediately notices that his bag is a good 30 kilos heavier than it should be and catches her. In the anime he brings her along anyway, whereas in the light novels he sends her back home.
Girlish Pigtails: One of Haruhi's haircuts. Also, Mikuru in her waitress outfit.
This trope is mostly invoked by Koizumi. Probably the most ridiculous is his line in "Endless Eight": "Perhaps grab her from behind, and whisper 'AI LAAV YOU' into her ear."
Kyon tends to speak English a lot too, mostly in "Endless Eight" - highlights are exclaiming "Excellent!" upon seeing Mikuru in a yukata, and his hilarious outburst of "Three days!?" when Haruhi tells him how long it took her to finish her summer homework.
"Groundhog Day" Loop: "Endless Eight", in which the SOS Brigade gets stuck repeating the same two weeks of summer vacation nearly 15,500 times and suffer from severe deja vu throughout — except for Haruhi, who remembers nothing, and Yuki, who remembers everything. The anime adaptation makes you feel it too, dragging the short story out beyond 15,500 and into eight repetitious episodes.
Groundhog Peggy Sue: See above. An interesting variation in that only one character is aware of the situation, and she is unable to take action herself.
Hands-Off Parenting: All characters' parents are so absent, they're not even mentioned. Yuki lives alone, being an alien, Itsuki's and Mikuru's parents are never shown, though presumably them being secret agents has something to do with their surprising amount of free time. Even Ordinary High-School Student Kyon is at home with his sister, but his parents are never seen. Both Kyon and Haruhi's parents are present (Kyon's sister often acts a a go-between for him and his mother-fetching him for meals, waking him up, etc-and is once even heard complaining to her one time when he kicks her out of his room), they're just unseen. Haruhi's mother is mentioned very briefly in the beginning of Surprise, where she's explained to be a Lethal Chef.
Heroic BSOD: Kyon is positively distraught in Disappearance when he finds no one remembers Haruhi or the SOS Club, to the point of shouting at and shaking people visibly frightened by his outburst.
Heroic RROD: The beginning of Book 10 reveals that Yuki's "flu" is a result of the Data Overmind using her in an attempt to contact/understand the utterly alien Canopy Domain. This weakens Yuki so much that she can barely communicate. More than usual, that is.
High School Hustler: Haruhi has gotten away with hijacking the literature clubroom, blackmailing the Computer Club President into giving a computer away for free by having him grope Mikuru, dressing as bunnies, submitting her film to the culture festival with the applications already closed...
Hostile Show Takeover: The entire plot of Disappearance. Yuki rewrites reality to change herself into the main character: a painfully introverted — but completely human — bookworm with a crush on Kyon. Meanwhile, Haruhi and Itsuki are Put on a Bus and Mikuru gets shipped with Tsuruya so Kyon can't get close. Got its own spin-off manga! Of course, once Kyon finds Haruhi and gets her going, she immediately sets out taking the show back for herself. Even in the official Alternate Universe manga, she seems poised to steal the spotlight...
Humans Are Special: Humans apparently are the only organic lifeform that can actively seek knowledge and continuously advance themselves.
I Am Who?: Haruhi Suzumiya. Kyon also occasionally discusses or invokes this trope when thinking about his own role.
I Choose to Stay: In The Disappearance of Haruhi Suzumiya, Kyon is given the opportunity to leave the SOS Brigade and Haruhi's fantastic world of aliens, time travelers, and espers, both of which he's complained about for the entirety of the series up to this point, behind him, and start a new life. The offer comes complete with new friends to make and even a potential love interest, but in one of the most moving inner monologues in the series, he decides that he can't leave that world behind, even going so far as to say he'd have to be an idiot to walk away from it all.
Haruhi lived a happy childhood until she discovered that her life was ordinary, and then decided that she would become an extraordinary person, or find extraordinary beings like aliens, time travelers, espers or sliders. She creates the SOS Brigade with that latter purpose. Subverted, however, because it turns out that what she most enjoys is hanging out with her fellow brigade members and doing ordinary high school activities together, like playing baseball, doing summer activities or helping them do their summer homework. So Haruhi is really I Just Want to Be Normal posing as I Just Want to Be Special.
Image Song: The amount of additional music done for the show is staggering, rivaling Mahou Sensei Negima!. 16 character albums, 4 soundtracks, 3 drama CDs, 8 combination soundtrack and drama CDs that shipped with one of the DVD versions, a live concert, and an orchestral concert.
First set: Haruhi Suzumiya, Yuki Nagato, Mikuru Asahina, Tsuruya, Ryoko Asakura, Kyon's sister, Emiri Kimidori, Itsuki Koizumi, and Kyon.
Second set: Haruhi Suzumiya, Yuki Nagato, Mikuru Asahina, Itsuki Koizumi, Kyon, Tsuruya, and Taniguchi.
Haruhi cuts her hair after meeting Kyon, about the same time she changes from being antisocial to being outgoing and happy. Before that, she changed her hair based on the day of the week, with a full-blown explanation as to why. It's implied she did this to get Kyon to comment on it.
Haruhi can sometimes be seen holding her hair in a ponytail after Kyon claims to have a thing for girls with ponytails in a "dream," with the most obvious example being that she has her hair in a ponytail the very next day after said "dream." In fact, at one point, when deciding on whether or not to put Mikuru's hair in a ponytail, Haruhi looks at Kyon and immediately drops the idea out of jealousy.. She does it again the day after Kyon blows up at her over her mistreatment of Mikuru during the shooting of their movie.
Improbable Age: Koizumi may or may not actually be the one in charge of his Organization.
Incest Subtext: Though Kyon is most definitely not attracted to his sister, he is attracted to Mikuru, and at least six times, he pointed out how similar she is to his sister, causing an inverted example of the trope. He also sees simularities between Haruhi and his sister as detectives.
Indecisive Medium: The Anime went out of its way not to show Kyon's mouth during his monologues, to keep the uncertainity from the novels, where you could never tell if he was saying something out loud, or just thinking.
In Sigh, Mikuru shows some rare outgoing qualities by offering Kyon a drink from a water bottle that she already drank from, and Haruhi grabs it before Kyon can. Subtextual meanings runs rampant among fans.
A straight example at the end of the last episode of Sigh, when they flashback to when Kyon talked to Haruhi at the cafe in May - Haruhi finishes Kyon's drink shortly before storming out.
A better example in book 6 (with free bonus trope). Mikuru places her finger on Kyon's lips and then her own, in order to get him to stop talking.
Invisible Parents: There are some parental figures, like the various adults in the island episode, but none of the characters' actual parents are ever seen. Yuki, of course, has no parents (in the human sense anyway) and Mikuru's probably haven't been born yet, but Haruhi and Kyon are implied to have parents...who never show up, (Kyon's mother is never directly seen or heard, but often referenced, and his dad is mentioned once) and never seem to say or do anything that affects the plot.