All Just a Dream: During Holiday Star, Hiyoko can discover Tohri's nefarious plot. Cut to her in a cafe with Ryouta and Kazuaki, saying "Crazy dream, huh?". Ryouta falls for this trope and gets told that she was joking. During the shrine visits, Yuuya halfway confesses to Hiyoko that he's not just an Ordinary High School Student, but chickens out and says he was talking about a dream.
All There in the Manual: The guidebook greatly expands on the characters' backstories, particularly Shuu's/Ichijou Utsuru's
Bad End: As usual for the genre if you don't go all the way with any romance.
There is also one caused in the demo version by staying in the infirmary to wait for Ryouta. Doctor Shuu cuts your head off and stuffs it in a box. The normal ending for Doctor Shuu might also be considered this.
Battle Butler: Sakuya's butler Albert Alain Alkan. Also a typical Scary Black Bird. He is actually an infamous assassin who was contracted to kill Sakuya, but later hired by him for protection.
Big Damn Heroes: On the Bad Boys Love route, just when things look at their bleakest with a trapped Kazuaki and Anghel dying from poison gas and a broken Ryouta submitting to Doctor Shuu, Oko San and Sakuya show up to help.
Blood Science: Mad Scientist Tohri Nishikikouji uses Anghel Higure's blood to help power his canon and materialize the will and drive of fanboys and fangirls, turning it into an offensive beam capable of destroying buildings.
Bread, Eggs, Milk, Squick: The various clubs at the school include the track team, the student council, and the birdwatching club... which, in a school for birds, basically amounts to voyeurism of (and by) school students.
Break the Cutie: Happens a lot in the Bad BoysLove route. Ryouta, however, by far gets the worst of it, particularly when the identity of Hiyoko's killer is revealed.
Breaking the Fourth Wall: Hiyoko is aware of the ending credits sequence that happens after getting Azami and Blaster together and interrupts it angrily. In Holiday Star's fourth episode she recaps the third one out loud for "the camera", and when Nageki asks about it she says people might have forgotten. He says being so aware of the camera doesn't seem very professional.
"Whatever! It's better to give the readers a hand!"
If you join the student council then you are forced into the vice presidency. Fair enough: you're the only other person on it.
A creepy example occurs during Doctor Shuu's best ending in the full version: when he asks you if you love him after he's killed you and is currently carrying your severed head around and interprets her head bobbing up and down in the jar as an answer, since your three choices all say "Yes." Worse: If he isn't actually carrying your head around at the moment of dialogue then that means he has attached it to Labor 9, or the Scarecrow. You can only answer "yes" because you don't have free will anymore.
Cerebus Syndrome: Most of the game is rather silly and lighthearted. Then you get on the Bad Boys Love route in the full version, or play the last chapter of Holiday Star...
Club Stub: The Student Council. If the heroine joins, there are two members. Otherwise, it's just Sakuya, who doesn't seem to be in touch with his class's opinions or even want to be there.
Coca-Pepsi, Inc.: A religious example. Hiyoko mentions that she comes from "Shint Buddhist" family. Both Tanabata and Christmas are celebrated in this universe. Anghel mentions reincarnation in his ramblings, but his human portrait also has crosses (a symbol of Christianity, a religion, which has nothing to do with reincarnation) and his name means "Angel" -angels belong to Abrahamic religions, not to Dharmic ones.
Cowboy Bebop At His Computer: One of the game reviews mentioned the protagonist's name - Cloaca Mahoney - as a downside. In fact, "Cloaca Mohoney" is only a name Angie Gallant chose for her famous walkthrough of the game. See, kids? That's what happens when you don't play the game before reviewing it.
Creepy Physical: The doctor, Iwamine Shuu, offers to give you some interesting drugs. He also promises to examine your insides most intimately once he's done preserving your head.
Cry for the Devil: Doctor Shuu appears to rocket-jump over the Moral Event Horizon in the Bad Boys Love route. Then he reveals that he's doing all of this because of his unrequited love for Ryouta's father and sincere desire to fulfill his dying wish. It doesn't excuse the horrific things he's done up to that point, but it does make one feel at least a twinge of pity for him.
Damning With Faint Praise: In the first scene with Ryouta, he offers to make breakfast for our heroine. Her answer? "Maybe I'll take you up on that, if starvation looms!" Ryouta's cooking is maybe preferable to starvation? Gee, thanks for that vote of confidence... Which is odd, because she says that Ryouta's cooking is delicious if she talks to him during the class hike. Maybe it was just her typical Large Ham way of speaking?
"That's terrible! I mean, Okosan is a nutcase and I don't know what he's saying half the time, but he really does like pudding!"
Don't Fear the Reaper: The Conductor in Holiday Star is pretty laid back and gives advice like "I dunno, kiddo. We never recommend haunting as a deathstyle choice, y’know? Too easy to go all black and bitter." It's revealed at some point that he is Death, as seen in the Bad Ends, and Hiyoko considers him her friend. They go all the way back to the demo version!
Dub-Induced Plot Hole: In the English translation of the demo, Kazuaki refers to the bird in his marked-out photo with female pronouns, implying that she was his dead lover. This became a bit awkward when the full game version came out and revealed that Kazuaki's photo was most likely of his dead brother Nageki. Fortunately, this was corrected in the separate English translation for the full game.
Empathic Environment: Holiday Star's Mount Pudi has rain on it when the emotionally troubled Nemo/ imposter Kazuaki cannot remember his real name.
The Throne Room on Holiday Star also Turns Red when The King turns One-Winged Angel in desperation to keep our heroes on Holiday Star.
Epiphanic Prison: Holiday Star is a place that traps souls who are emotionally troubled and/or weak willed. The only way to leave this place is if enough of the trapped nindividuals realize they have something worth living for in life/reality/outside Holiday Star.
If you take the Bad Boys Love route, the game shifts from a humorous pigeon dating sim to a dark mystery/thriller.
Holiday Star's first two stories are loony absurd adventures, with minor darker hints here and there. The third story is similar, a fantasy-RPG-ish romp. Until the end of that one, and the fourth is nightmarish and aferlife-y.
100% Completion: Getting at least one ending for each bird unlocks the Bad Boys Love route, and completing that in turn gives you a "thank you" picture after the credits a full set of documents in the Library. Getting all of the endings for each bird unlocks a post-BBL epilogue, the last Gallery image, and a Library item with a bonus scene.
In the main game, only the protagonist and Anghel can see Nageki, though Anghel only shows this once as an optional scene on his route. During the BBL route, it is revealed that Ryouta can as well. Also referenced in the Drama CD when he talks to his "dead friend" Nageki in the library about one of the seven mysteries of the school: students who draw in library books are said to get cursed. As Ryouta suspects, there is actually some truth to this...
In the manga, Okosan can also see him, and in Holiday Star it's said that only the pure of heart can see ghosts.
Killed Off for Real: Hiyoko and Yuuya on the Bad Boys Love route. Although if you get the full ending, you find that Yuuya was saved just in time, and Hiyoko might be revived.
Killer Rabbit: You will never, ever look at Chukar partridges the same way again. Or King Quails, especially the darker colored ones.
A group of fans known as Team Hatoful has done a series of voiced playthroughs of different routes of the game - specifically Anghel's, Bad Boys Love, Ryouta's and Sakuya's routes, and has also completed a blind run of the sequel, HolidayStar. Notable for, among other things, taking Yuuya's Handsome Lech tendencies even further, giving the French Sakuya a fake British accent, and making Shuu sound like Severus Snape.
Lighter and Softer: The drama CDs and - for the most part - the manga are pretty much played purely for comedy and don't have the same tendency for twists and pathos as either of the games.
Meaningful Background Event: Blink and you'll miss it, but your first clue that things in this game aren't quite as cheerful as they first seem comes when Hiyoko decides to go for a run: One of the things she passes is the post-apocalyptic remains of a city.
Meido: Ryouta dresses up as this, and Hiyoko can join him.
In the bonus content you unlock by completing Bad Boy's Love, Sakuya and Kazuaki are dragged into it as well.
The Merch: There are already plans for tote bags, pins, St. PigeoNation ID cards and more. Various styles of St. Pigeonation bags, shirts, cups and even a thong with Yuuya on it can be found at the Cafepress store
Missing Mom: If you focus on Ryouta, then you find out his mother dies.
Mood Whiplash: The endings of Ryouta and Nageki's routes can come as quite a shock if you've grown used to the game's silly and comedic tone. The Bad Boys Love route in the full version, even more so. The manga, which is largely cheerful absurd short comics, also has several chapters end with Kazuaki explaining the history of the setting - like how a plague swept humankind and killed seventy percent of them.
"Not Making This Up" Disclaimer: The official website has many of these. People trying to get others to play this game typically have to use lots of these too, as most rational people's initial reaction to hearing about it is something along the lines of "Wait, something like this actually exists?!?"
Official Couple: It's not definite, but Ryouta seems to be the most canon love interest for Hiyoko as he's the one who stays with her spirit in the hopes of him being able to be cured of his disease and her being able to be transplanted into a body someday in the good ending to the Bad Boys Love route, the last route you can unlock.
Holiday Star suggests that it's Nageki, or at least has Ryouta fear this, but the Holiday Star route is distinct and doesn't overlap.
Ominous Save Prompt: This happens at the end of every chapter in BBL. This is also the only time players can save during BBL as well.
Bird of Mass Destruction: The Bad Boys Love route reveals that Nageki harbored a disease that caused all humans who got too close to him to drop dead on the spot, which was the main reason he killed himself. Unfortunately, some of his body parts were saved by Doctor Shuu, who intends to make Ryouta the new carrier...
The Promise: The Bad Boys Love route is jumpstarted by one.
Pun-Based Title: The title is a mix of hato, the Japanese word for pigeon/dove, and "heartful". The paid version of the game is subtitled "-Hurtful Complete Edition-" as well. Then there's Hurtful Boyfriend and Operation Hurtful.
Punch Clock Villain: If you don't finish any romantic storylines, a meeting of the Hawk Party condemns humanity and orders them exterminated... then adjourns for coffee.
Punny Name: The (quail) teacher and (partridge) doctor have surnames punning on the Japanese for "quail" and "partridge". The library freshman's personal name is based on "nagekibato", the Japanese word for "mourning dove". Both the partridge and the quail are operating under assumed names, so this was probably deliberate on their parts.
Rainbow Speak: On the Bad Boys Love route, several plot-important phrases are highlighted in yellow. Really important things are highlighted in red.
Played for Laughs as they are not very important: "Hiyoko levelled up! Wisdom increased by 5!"
They become a bit more important in the full version where you need to boost the appropriate stats to get the best endings for Doctor Shuu, Sakuya, and Oko San. Additionally, Anghel's route features a turn-based RPG battle and while it's mainly used for parody, it is possible to lose it and get a bad ending if you botch it.
Save Game Limits: The Bad Boys Love route, in contrast with the main Otome route where you could save any time you wanted, lets you save only at certain points in the story.
Probably his best, however, is unleashed upon Sakuya on Oko's route if you side with him during an argument between the two: "GIGA...DRILL...BEEEEEEEEEAK!!" Sakuya doesn't have a prayer after that one.
Another Pokémon reference in Yuuya's route, followed immediately by a Toy Story one: "Blast off at the speed of light! To the maintenance office and beyond!"
Star-Crossed Lovers: Anghel claims that Hiyoko and himself were this in a past life. A more straight example would be Hiyoko and Nageki on Nageki's route when he fades away after realizing that he loves Hiyoko.
When the heroine shows up on the wrong day for class, if you choose to return home, she tells Kazuaki: "I must return to my people with the spoils of war, lay my bloodied sword at the feet of my great king, and celebrate my conquest of all the lands from here to distant Macedonia."
Except for the student festival in fall, when your class does a Maid Cafe and Ryota briefly appears with a maid outfit drawn over his photo. This leads to the usual fanart of everybirdie crossdressing as maids, even those in other classes and the staff. Oko also appears in a maid outfit during his route, and the Library menu's post-BBL bonus scene shows Sakuya and Kazuaki as bemaided birds as well.
And Oko San's ICPSS portrait, while all other characters are rendered as Bishounen, is a bird in a school uniform.
In the full version, you can see the other classmates dressed up as maids for the Maid Cafe, and Ryouta fills in as a Miko at the local shrine for New Year's.
During the Radio session for Holiday Star, Ryouta explains that clothing isn't mandatory for birds, who wear clothes for protection against cold, fashion, or ceremonial purposes only.
Tempting Fate: In Holiday Star, Sakuya proudly boasts that there's no way the thieves will be able to get into the council room. Hiyoko refers to this as "raising a flag", and when the inevitable happens she and Ryouta call it "flag retrieval" - they're terms commonly used to refer to visual novel gameplay.
Two-Teacher School: The main game has only Kazuaki and Shuu. BBL shows us the principal, but only briefly and not while he is still among the living.
Uplifted Animal: It turns out that intelligent birds did not naturally come about...
Widget Series: The premise of the game is considered to be very far outside the mainstream box.
You All Look Familiar: The manga lampshades the difficulties of having three white fantails in the cast, and distinguishes them by giving Sakuya and Yuuya accessories in bird form, while Oko San remains "nude". Less present in the actual game where their bird-photo images all have different poses, and of course their human-style portraits are all different.