Adult Fear: Really sets in with the gradual mind-wiping of Wildseeds' families. Imagine your child went off to a boarding school. You dropped them off there, you could drive back, but you can't remember a damned thing about it. You can't recall anything specific about the place and, even worse, as time goes on, you have no want to visit or see them at all. Eventually, you can't really remember caring about your child at all and may, some day, forget about them altogether. And the magic community pretty much sees this as acceptable.
Also the inverse situation: A child of a witch family is given a choice at 13 whether to keep their magic - and if they choose not to, they have to forget everything magical, including their parents and family. One momentary decision by your just-teenager child, and you'll never see them again, or if you do they won't remember you, and you won't be allowed to show you remember them.
Animal Motifs: Deliberately invoked by the faculty of Iris Academy. All students are assigned a house when they enroll;
"Adventurous" Horses, "charming" Butterflies or "mysterious" Snakes for the girls
"Daring" wolves, "elegant" falcons or "eldritch" toads for the boys.
Bonus points for one of the characters from Butterfly Hall having literal wings.
Possibly also Damien, depending on how you choose to phrase the love letter and whether or not you're just making things up. "Voice like melty butter," indeed.
Asexuality: Virginia repeatedly insists she's not interested that way in anyone, male or female. Even if you manage to enter into a romantic relationship with her (which isn't easy), at the end it comes out that she'd really rather just cuddle.
Crapsaccharine World: It's such a pretty magical world, with freaky yet lovable characters, fairy wings, and Troubled, but CuteBishōnen. Yet magical society is exceedingly totalitarian, its rules are enforced by Laser-Guided Amnesia, the students at Iris Academy have very few rights, and even then, the professors are not the ones who are the most dangerous to you.
Crippling Overspecialization: If you don't at least take a look at all five magic types early on, you'll get detention or demerits. Also, not all dungeons can be solved by all kinds of magic, so someone who purely specializes in a single art is at risk of demerits.
Depraved Bisexual: Damien. If you don't romance him, he'll go after a freshman boy instead. On the other hand:
Everyone Is Bi: Gender appears to be completely irrelevant when it comes to romance here; not only can characters be romanced either way but no one comments on this to indicate that it's at all unusual, and other NPCs date both genders as well. Most obvious with William, Damien, or Ellen if you pursue her.
When Jacob's "fathers" are mentioned in Virginia's path, it comes up very casually and might not even be noticeable if one doesn't pay attention to his exact wording (as in, "my fathers" versus "our fathers").
In fact, is a minor plot point. Mary catches Virginia and the fairy-girl complaining about how the new class is mostly girls, and how this means the fairy girl will, essentially, have to go 'the other way'.
Damien. Alienated from his muggle parents? Check! Bullied at school due to his mysterious, demon parentage? Check! Believed to be a vicious The Casanova - while really just Looking for Love in All the Wrong Places and getting his trust betrayed constantly for his trouble? Check! Too bad it's an act he puts on, specifically designed to invoke this trope.
Foreshadowing: If you manage to acquire certain amounts of magic points before the events, some of Ms. Potsdam's lectures can be considered foreshadowing at least for Damien's path, and possibly a few others'.
Gay Option: No Hanako Games title would be complete without this. In this case both Ellen and Virginia fulfill the role officially.
Jerkass Has a Point: For all of Damien's flaws and problems, it's safer to listen to his warnings:
Your first encounter with him in the gym, where he tells you to attend at least the first lecture of every class and not trust the professors? You need a minimum of one point in every colour to avoid getting detention after the first two weeks, and a minimum of ten to avoid being kept behind for summer school. And Potsdam definitely isn't telling you everything.
His suggestion to study blue magic during Initiation week? Successfully using blue magic (which requires a total of thirty or more points in it) will get a whopping ten merits in the first exam - more than you can get from any other option.
His warning not to use Spirit Sight during the Dark Dance? Doing so will turn you blind and cause Grabiner to give you detention and take ten demerits from you - twenty, if you'd mentioned the Dance to Grabiner prior to attending it.
Him telling you that you might be in danger in the Academy - that you could lose your mind, or your life, or worse? If you get expelled, you will "lose your mind" by being brainwashed. As for your life and your soul, they are also in danger... from Damien!
May-December Romance: You have the option to send a romantic valentine to Professor Potsdam. If you do, she turns you down. Not because she's probably old enough to be your mother or because a relationship between a student and teacher would be wrong, but because she doesn't want students thinking they can buy scholastic merits. She does seem genuinely flattered by the interest, though.
Odd Couple: You have two roommates. Virginia is a Book Dumb junk-food-addict slob. Ellen is a quiet, studious neat freak who loves vegetables.
This isn't quite Tomboy and Girly Girl since as Horses they're both somewhat tomboyish. Ellen is more girly, but not drastically. However, Pastel is extremely girly, and she and Virginia are apparently friends.
Parental Abandonment and Parental Neglect: Combined with Adult Fear for bonus points: the Masquerade reinforcement causes your parents - and the parents of every other Wildseed to forget that their kids are magical. In some cases, the spell hits so hard that the adults in question actually forget so hard that, at best, they forget why they care about the kid...and Ellen suspects that this is what's happened to her family. She later has Potsdam make them forget her completely and elects to stay at the school over the summer; if you've become close friends with her or are pursuing her romantically, you can offer to let her stay at your home during the summer - otherwise, you never even find out about the situation. More, it's implied from the way Virginia tells you this, that this is considered completely normal and justified by the born-witches.
Pronoun Trouble: Not all mages or magical creatures are male or female; some are asexual, hermaphroditic, have Bizarre Alien Sexes, or otherwise don't neatly fit into the human gender spectrum. Accordingly, Potsdam says that you should ask someone what they want to be called if you're not sure, and also mentions that mage society has worked out a gender-neutral pronoun system ("e" and "eir" for "he/she" and "his/hers," among others). It isn't a big deal in-game, however.
Minnie uses the gender-neutral pronouns in a conversation with you if you're on the student council, in an attempt to conceal that she's asking for advice about her relationship with Kyo.
Revenge: The raison d'etre of the Rose and Wasp. However, their involvement almost always leads to something the player will regret.
Running Gag: "...Wait, is this going to be sex education!?"
Save Scumming: Given the multiple dialogue options, multiple game paths, and random nature of magic skill gains, this is pretty much required. Given that you can literally save everywhere, to 80 slots, this is also practically a game feature.
Secret Character: As of the latest patch, Big Steve now has a partial romance path. Reaching it is much more difficult than any of the other characters.
Shiny New Australia: When Damien starts sending you letters, he says he is willing to conquer the world for you. Then again, he might have planned to anyway.
The Talk: Something of a Running Gag. Professor Potsdam will sometimes open a class sounding like she's about to lead into the talk, only for it to turn out to be something unrelated. She does eventually get round to it, kinda. Apparently there are no rules against any kind of love in Iris Academy, but no student is allowed to carry children.
The Un Favourite: Ellen's comments to Donald, when the topic of sibling rivalry comes up, suggest that she either was this or at least feels like she's this. Coming to Iris Academy doesn't seem to have improved matters much - her family tells her not to come home for Thanksgiving. She eventually has Potsdam just make them forget her entirely.
What the Hell, Hero?: Happens very late into Damien's path if you try to appeal to Potsdam to let him back in for the May Ball. She not only refuses but very gently chews you out for even asking, pointing out that what he did might have been technically legal, but he still nearly killed you and he'd be expelled for that alone even if his deed isn't on the books as being expulsion-worthy (and if it isn't, she'll add it). On top of that, you realize - too late - that you just got told off in front of the entire school, and Virginia and Ellen very quickly find out. They are not happy to hear that you're even talking with Damien again after what he did to you, and refuse to listen to any justifications. They even kick you out of the room for good, only letting you back at night so you can sleep and their very justified fury carries all the way into the final exam - which they will deliberately throw unless you promise to break up with him right then and there. And breaking that promise deprives you of your magic - refusing to make it at all means that your entire Hall is so disgusted with you that the only option for you is to be moved to Snake Hall. "Perhaps the girls there will be more understanding of your choices."
You can get this from Minnie too, if you successfully campaigned for treasurer and try to use empathy on her when she comes to you with a problem. Turns out that doing that kind of thing is considered a bit rude in magical culture.
If you completely foul up an exam, Grabiner will pointedly ask just what the hell you thought you were doing, and remind you that the professors won't always be there to save your hide.