Taking the Bullet: Subverted. Yuki doesn't sustain lasting damage shielding Kyon with her own flesh.
Talking Is a Free Action: Somehow, Kyon in the anime, when thinking or narrating (you can hardly tell the difference between the two). Especially obvious during "Someday in the Rain".
Tanabata: One of the festivals the SOS Brigade celebrates in Bamboo Leaf Rhapsody. Also the day when Haruhi first met Kyon.
Team Mom: Haruhi is actually turning into this, starting around Disappearance, but especially obvious in the preview chapter of novel 10.
Technobabble: Every time Yuki, Mikuru and Itsuki explain something to Kyon, who normally lampshades it.
Technology Porn: The futuristic videogame "world," with tons of ships and views of torpedoes being loaded everywhere.
Temporal Paradox: Future Mikuru would not have showed her star-shaped breast mole to Kyon as a Trust Password if Kyon didn't tell Present Mikuru that she had one after Future Mikuru told him, because she didn't even know until Kyon told her.
Or rather, Tempted Fate. In the infamous "Endless Eight" arc, Koizumi said that Haruhi is so happy and could not possibly do anything horrible. Guess what happens.
"Stop yelling contest over and over. If those words reach Haruhi's sharp ears..." [HARUHI KICK!]
In Kyon's opening narration in the very first episode, he says he just wants a quiet life, passing through high school uneventfully. Then he meets Haruhi...
Real-life example: When the first Endless Eight episode was aired and it didn't end the plot conclusively like the original novel did several fans jokingly said that there'd be Endless Eight repeating for the whole season. Others jokingly responded that KyoAni would never do such a thing. Guess what happens.
Mikuru almost catches Kyon looking at his folder full of pictures of her, but he quickly closes the window, thinking smugly that he doesn't make mistakes. Immediately...
Mikuru: Huh? What is this? This MIKURU folder. Kyon: Gah! I slipped up.
Time Travel: The novels get really complex about this later.
The Door Slams You: Kyon happens to be leaning against the clubroom door the first time Haruhi yanks it open. It opens inward, slamming him against the floor rather than the wall. He avoids the door after that.
The Glomp: Mikuru does this to Kyon after the Melancholy finale. She then immediately lets go because she doesn't want it to happen again..
Theme Tune Cameo: Kyon's sister hums "Bouken Desho Desho" in "Melancholy VI", and Haruhi sings a few lines of "Hare Hare Yukai" while stripping Mikuru in "Someday in the Rain".
There Are No Therapists: Early Haruhi hit a fair few points of the criteria for Psychopathy (or similar social disorder), and as far as we know, never gets taken for therapy of any kind, even though she really could have used it. Then again, you could make a decent argument that Kyon is acting as her therapist.
Twice called out over Yuki Nagato's name in the books, once in Wavering and again in Indignation.
Mikuru's name can be read to mean "Sees it coming."
Kimidori can be read to mean "green" — something lampshaded in Haruhi-chan.
Itsuki means "tree." Mori means "forest."
There is a large hotel chain in Japan named "Tsuruya" (similar to Hilton or Marriott in the United States).
Haruhi itself means "spring day" (as in the kind of day that makes one energetic) and can also mean various things depending on what kanji are used.
This Is a Work of Fiction: In Sigh, Kyon actually uses this to save the world from talking cats, Mikuru Beams and autumnal cherry blossoms.
This Is Unforgivable: Movie!Asakura's way to vaguely threaten Kyon should he happen to start dating Yuki and not take it seriously. The official English translation in the novel is a bit less threatening ("...if you intend to go out with Nagato, you'd better be serious about it. Or else I won't allow it.")
Those Two Guys: Taniguchi and Kunikida — though we see a lot more of Taniguchi.
Tin Man: Subverted with Yuki, who legitimately appears to lack normal human emotions... at least, at first glance.
Subverted in the first few novels, at least for a while; neither Itsuki nor Mikuru trust the other fully, if at all, and Yuki warns Kyon not to trust anything any member of the SOS Brigade tells him. Kyon in particular is annoyed by most of the members, particularly Itsuki and Haruhi, and explicitly only cares about Mikuru, and regards Yuki as no more than a part of the furniture. The fact that the entire group has been brought together against their will is often a point of contention, and though Haruhi treats the group as True Companions, no-one else sees it as such until Disappearance. After that, however, the characters begin to treat each other in a manner that befits the trope, with Itsuki in particular saying he would gladly betray the Organization for the SOS Brigade.
The 11th book REALLY showcases this trope, with Itsuki once again being the main one to show it, saying that the SOS Brigade has become a part of him now.
True Love's Kiss: Kyon kisses Haruhi to convince her to turn the world back to normal — or at least give her an interesting romantic subplot with Kyon, keeping her from getting TOO bored.
Adult Asahina attempts to use her mole as a Trust Password with Kyon. It doesn't quite work. Similarly, in the movie, Kyon tries to use this with younger Asahina, but it doesn't work out either.
In "The Melancholy of Mikuru Asahina," Kyon says that his option of telling Asahina his knowledge of her future self is a trump card comparable to telling Haruhi that he is John Smith.
Kyon might also be the key to unsealing Yuki's full power. Yuki says she has willingly sealed off her ability to synchronize, and that she cannot unseal it herself. She says the password to unsealing is in someone else's hands, but doesn't actually say who.
The fans who want Kyon with Yuki (also hinted by the series) notice the all-powerful data entity probably doesn't want to see Yuki actually liking someone. SHOCK. And loli-Mikuru can't have any (sex) relations with anyone not from her future.
Unfamiliar Ceiling: The Disappearance of Haruhi Suzumiya combines this with Timey-Wimey Ball. Kyon wakes up after experiencing being stabbed by Asakura, but by the time he wakes up, the past has been rewritten so that he fell down a set of stairs and hit his head.
Unfazed Everyman: Kyon, quite obviously. He's quite Genre Savvy about it, too, although having a world-changing demiurge as a friend/boss kinda forces him to be.
Unreliable Narrator: Kyon is odd. There are contradictions and quirks in what he says as a narrator and as a person that are just out of place.
Unreliable Voiceover: Sometimes Kyon's narration is contradicted by what's on the screen, with no reason to doubt that the visuals are anything other than the truth. The best example is in the first chronological episode, when he says he's not interested in Haruhi, despite having just spent several scenes very obviously checking her out.
It largely seems like nobody who hasn't had the Masquerade broken for them can connect the dots and notice the weird events that happen around Haruhi for what they are. Events or situations where this is evident:
Haruhi's herself, of course. Most incredibly in the "Snow Mountain Syndrome" story.
Many of the supernatural events in Sigh happen in the presence of Haruhi, Tsuruya, Taniguchi, Kunikida, and in one case the whole city, who either don't notice them or come up with mundane explanations for them (for example, "the fence must be really old" when it breaks in perfect, neat lines due to Mikuru's cutter beam).
Nagato's performance in "The Day of Sagitarius."
Nagato's "ventriloquism" in the student movie.
The SOS Brigade's baseball game — though the Kamigahara Pirates become superstitious about Kyon's bat.
Possible exception: Tsuruya, as seen in Novel 7. She knows that the SOS Brigade isn't normal, but we don't know whether she's figured it out on her own, or whether she's been told.
To start with, Melancholy, part 5. Now that is how you peel back a masquerade!
The biggest Wham so far, though? Disappearance, entirely, in both book and movie form. It's basically three hours of having your face hit with a sledgehammer over and over — and you'll love every second of it. By the end of it all, everything you knew about the universe of the show has been turned on its ear and all previous suppositions are called into question.
Book 10 pulls this off rather nicely too. It's even called "The Surprise of Haruhi Suzumiya". Fujikawa is trying to give Sasaki Haruhi's power so he can control Sasaki and resurrect his sister—who is an alternate timeline version of Mikuru. Except it completely fails, because Haruhi saw this coming, split the timeline a week ago, and created an avatar that could consciously wield her powers to save everyone.
What Happened to the Mouse?: Shamisen, the talking cat, appears in episode zero (eleven chronologically) of the 2006 version of the anime, in the opening and ending animations, and nowhere else in that season. It's implied that Kyon takes the cat home with him after the filming incident, but he's never seen at their house in the later episodes (most of which take place earlier in the year). This can be confusing to first-time viewers, who might think of this as clumsy continuity until they figure out the gimmick of the first season. The 2009 version of the series, however, inserts the episode that introduces Shamisen into the proper place in the chronology. Amusingly, the short story that expands on Shamisen is called "What Happened to the Cat?"
Why Don't Ya Just Shoot Him?: Despite having "total data jurisdiction over [the classroom],"Ryoko insists on using her military knife to do the deed when she obviously could've crushed Kyon with flying desks (or done anything else, really).
Wife Husbandry: Time traveling high school boy encourages junior high school girl towards the topics of his interest.
Woman in White: Haruhi during the prologue of "Remote Island Syndrome".
Woobie, Destroyer of Worlds: After going through nearly 15 and a half thousand of the same 2 weeks, Yuki gains emotions and becomes this. Except that she doesn't destroy the world. She steals Haruhi's powers and retcons reality for 1 year, according to the novels, and 3 years and 5 months, according to The Movie. And she succeeds. And she's stopped by the protagonists. And, for a point in time, there's 4 Kyons and 3 Mikurus.
The Worf Effect: Happens to Nagato with the Sky Canopy Domain, both in Snow Mountian and Surprise
You Didn't Ask : Endless Eight would have been a lot shorter if someone just asked Yuki. Justified in that her role is to observe. Subverted when a Genre Savvy Kyon uses this to help solve the Remote Island mystery. Itsuki asks Yuki for a body's temperature to estimate the time of death. Kyon later realizes that she would have just told them the time of death if asked directly (remember her fortune telling?)...which would have revealed that the person was not actually dead.