All Just a Dream: The entire first segment of episode 12. Of course, Mariya and Matsurika were somehow able to see everything in the dream and tell Kanako exactly when it started. Becomes a running gag in Alive whenever Jayano Enjouji shows up. Implied, but not stated when she appears in episode 12 during Kanako's birthday party.
An exception is Mariya: his crossdressing seems more tied into his planet-sized ego. And despite being in an all-girls' school, he's never actually done anything with it. If anyone's a pervert, it'd be Kanako (Good Lord, it'd be Kanako...)
Bokukko: In the manga, Shizu makes appearances dressed as a boy, and uses "boku" accordingly.
Brick Joke: The pendant is noted as being significant in an early episode and in the very last; it's subverted because we only get to see Shizu gasp in shock upon seeing it and the show ends before she can say anything about it.
But Not Too Foreign: Father Touichirou Kanae is part-French. Mariya and Shizu had an Italian grandmother.
Butt Monkey: Kanako gets mistreated by most peers (except Kiri, Sachi, Yuzuru and Ryuuken), mocked constantly by Mariya, insulted by Matsurika, developed an allergy to boys as a result to being teased by them... as some would say, she is Yukinari's soulmate.
Cool and Unusual Punishment: For her crime of biting Yonakuni (which, as he is a pet, is counted as personal property damage in Japan), the jury for Kanako's trial in the fourth episode of Alive sentences her to... a night getting lectured by Father Kanae. This also prevents her from studying for exams.
Comedic Sociopathy: A very disturbing example, if you think about it. Mariya psychologically harasses Kanako with zest, partly so she wouldn't reveal his secret, but partly for the pure amusement. This involves things like showering Kanako with gasoline and waving around a lighter, until Kanako "apologizes for her behavior". Kanako is practically reduced to a obedient serf by a mix of blackmailing, bullying and seduction. Remarkably, the show manages to remain a tongue-in-cheek comedy.
The opening for both seasons ("Hanaji" and "Runrunriru Ranranrara") are sung by Yuu Kobayashi, and the second season's opening for the first 2 episodes ("Mousou Senshi Miyamae Kanako") is by Tomokazu Sugita.
Empathic Environment: During Kiri's discussion with Kanako in Episode 4, the background changes depending on what was said.
Even Bad Men Love Their Mamas: Mariya loves his late grandmother so much he agreed to the crossdressing, cross-school competition with Shizu, but doesn't mind whether he wins or not, seeing it as more of a fulfilment of her last request.
Failed Attempt at Drama: Shizu tries a tearful, dramatic exit after she felt insulted by Mariya's gesture to cede his chairmanship for both schools to her by asking her to kiss his feet... only to realize that she forgot to keep the door open.
A God Am I: God the Dorm Leader may be appropriately named, seeing as Heaven and Earth will move themselves to acquiesce to her desires. She can even dissipate a June rainstorm just because she didn't feel like hanging out in Mariya's room anymore after they ran out of snacks.
She is also hinted to actually BE God, among many other things, like possessing time-warping powers and having been very deeply embroiled in the history of ancient China.
Goofy Print Underwear: Ayari's panda-print panties, which are accidentally exposed by Shizu (posing as Mariya) when they were children. She has since hated him for that incident.
Groin Attack: How Kanako further verified the fact that Mariya's a crossdresser, by grabbing his... magic stick.
Kanako: "What the hell is that thing beneath your skirt?!"
Mariya: "Now you've known it..."
*Kanako removes her hand from beneath Mariya's skirt and groans as she waves her hand*
Half-Identical Twins: Shizu, Mariya's twin sister who looks all but identical, except she's an actual girl (and is Mariya's complete opposite personality-wise). Also, Mariya has a mole under his left eye, while Shizu has one under her right.
Hammerspace: Kanako tries to work out just how Mariya could hide an entire second room behind the dressers in their room, said dressers being set against the wall that connects to the outer hallway.
Mariya: "Do you know how much I had to spend on this?"
Also, Sachi's left pocket from where she can pull whatever is needed in any situation.
Heir to the Dojo: Their late grandmother's will subjects Mariya and Shizu to an inheritance competition in which both are to attend single-sex schools (both of which their grandmother once served as chairwoman) whose gender population is opposite theirs and under each other's names. Thus, Shizu attends the all-female Ame no Kisaki as "Mariya", while Mariya attends the all-male Mihoshi no Mori as "Shizu". Whoever keeps their gender secret for the next three years wins chairmanship for both. Shizu claimed victory due to Kanako learning of Mariya's gender. The latter, however, pulls off a comeback victory due to an indisputable technicality: Kanako learned of his gender before he attended school (and is currently blackmailing her into keeping it a secret), while she learned of Shizu's while she's already in school. Nevertheless, he's willing to overlook this technical victory in favor of Shizu... by asking her to kiss his feet.
Hot for Student: Father Kanae has some unspoken feelings for Mariya while being completely unaware of "her" actual gender.
Kanako's parents also met this way at Ame no Kisaki: her father was her mother's teacher, and Kanako's older sister was born when her mother was sixteen and had gotten married.
Huge Schoolgirl: Kanako and Ryuuken. Kanako is especially embarrassed about her height.
Hypocritical Humor: Kanako states that she hates those who "get excited by high school girls exposing a bit more skin due to the seasonal change of attire." Considering what she just did a bit earlier in the episode...
There's also Mariya constantly insulting Kanako for being a disgusting pervert. Coming from a guy who seems to have come to enjoy his life in drag.
Japanese Pronouns: While keeping his "good girl" masquerade, Mariya speaks with "watashi" and uses polite speech. When around people who know his secret, his speech is rude and masculine and uses "ore" accordingly.
Pet the Dog / Jerk With A Heartof Gold: On the other hand, on occasion he exhibits a genuinely nicer side. He doesn't mind having to take heat from Ayari on Shizu's behalf after the latter accidentally exposed Ayari's panties as children, is willing to cede chairmanship to Shizu, saves Ayari from falling off her float, and, despite enjoying torturing Kanako psychologically and emotionally, he frequently gives her helpful advice. Of course, he's quick to explain away all these rare instances of kindness on his part as a façade-maintaining measure.
His heart of gold is showing out more in Alive. For instance, he always bails Kanako out of problems she accidentally caused herself, even if he need not to, like her dilemma over her gift for Sachi for the latter's birthday and the conundrum that arose concerning her own birthday when she was unwittingly leading people on.
Also despite making fun of Kanako for being a lesbian, he doesn't seem to really mind it, being more disgusted by her perverted urges. He even tries to stop her when they are about to go out of controll like in episode 10.
Lovable Sex Maniac: Kanako, though mostly to Mariya, says some perverted things without a second thought, and joined the school specifically to hit on girls.
She even spends the first chapter of the manga acting exactly like her straight male counterparts...and they react to her the same way they would to a man.
Love Letter Lunacy: Kiri gets a letter from a man she met on the train and tries to reject him, but it just doesn't work. Kanako remains in the dark during this entire segment. Then a letter from the man ends up with Sachi...
Medium Awareness: When one episode has pop-up notes on idioms and other random factoids, Mariya and Matsurika somehow become aware of them towards the end of the episode. Mariya himself indicates he cosplays in maid and nurse outfits to provide fanservice during an episode, noting how little screentime he's gotten.
In episode 4 of Alive, Kanako comes to the conclusion that Mariya is prosecuting her because he wants her spot as the main character of the show (which isn't helped by the fact that his name is on the title). Matsurika just tells her that it's the least of her concerns.
In episode 8 of Alive, Mariya and Matsurika are so disgusted with Kanako that they revoke her right to speak for the entirety of the next episode. Sure enough, she's being prevented from doing so.
Meganekko: Kiri is even called one when Kanako first sees her.
Nosebleed: Kanako. Frequently and with such force that she rivals Ikuto. Also the name of the first season's opening theme, for that very reason.
When she volunteers to help with the girls' physical examinations she actually ends up in the infirmary after blacking out from blood loss.
Stains the left cheek of a statue of the Virgin Mary with her blood after seeing Ayari's Wardrobe Malfunction (and consequently becoming one of their school's Seven Mysteries).
And she turns the whole world red from a nosebleed in season 1's final episode.
Not Distracted by the Sexy: Mariya has shown no perverse inklings at all despite the opportunities his venture could present. Hell, beyond taking the time and effort to mess with Kanako (and maybe Shizu and Father Kanae), he's a model student and an Onee-sama to boot.
Ojou Ringlets: Ayari's curls remind Kanako of chocolate coronets.
Older than They Look: God and Yonakuni. The paper from a love letter God/Dorm Leader got long ago has already rotted, and the only difference from then is the fact that she wore clothes from what looks to be pre-War Japan.
Schoolgirl Lesbians: Kanako. Though she prefers not to be called that.note Probably because the word "lesbian" has different connotations in Japanese as in English, at least to judge by Kanoko's reaction.
The Seven Mysteries: Kanako is responsible for all of them, generally due to profuse nosebleeding. Kumagai-sensei later tells her that the school's seven mysteries change annually, but seven other mysteries about God have never changed, ranging from the genuinely mysterious ("How old is she?") to mundane Fridge Logic ("Why are Virtual Boys not banned along with the other electronics?": she later claims she likes things with a tragic history...). If anyone happens to learn all seven mysteries, the dorm manager will do... well, something, anyway.
Serious Business: Shizu's attitude towards the inheritance competition. Mariya thinks otherwise.
Miyama (no e) Kanako was a heroine of a visual novel called Atlach=Nacha. She's the servant of a demon-spider girl.
In episode 5 of Alive, the punishment of watching the entire "Legend of Japanese Heroes" back to back without blinking mentioned by the Dorm Leader is a spoof of Legend of Galactic Heroes, which in fact, if one includes the side story episodes, really consists of 165 episodes.
Shown Their Work: The writers are aware of what Christianity is, and a rare serious moment has Ayari explaining to Kanako just who "Maria-sama" is; the origins of Christmas, and how non-Christian (like most Japanese) students get along with the Catholic school's nuns-and-rosaries environment. (Even if one isn't praying to a specific God, you can be thinking about friends or loved ones, or reflect on your behavior with others.) Also, it's explicitly stated that the nuns do not force their beliefs on anyone.
Alive also mentions how crash dieting isn't helpful and often just leads to problems and one can possibly rebound, and gives a basic outline of how dieting should actually go (namely [paraphrasing Mariya]: following a sensible plan, cutting back caloric intake and exercising properly). The entirety of the next episode is dedicated to the consequences of Kanako's forced diet.
Totally Radical: Father Kanae tries talking this way with Kanako in the dub, "Dawg, how you doing!?"
She tries to respond the same way. Both then agree to stop. The audience thanks them.
Tsundere: Matsurika refers to herself as "100% tsun with no dere at all."
Kanako herself calls Mariya one (at least deep in her head) given Mariya's behavior towards his female relatives (e.g., twin sister Shizu and cousin Ayari). He also tends to explain away any good behavior towards his classmates as a face-saving measure for him and/or the school, possibly in order to cover-up his deep-seated sense of kindness. Of course, he'll complain all the while... even as he saved Ayari from falling off a float during a Catholic festival.
Unflappable Guardian: God. There is nothing she doesn't know and nothing she will let her students get away with. Unless they get away with it cleverly.
She'll still catch them, of course, but if they at least put enough effort into it, she'll give it back.
And she gives points for creativity in hiding, and also has retests.
Unsettling Gender-Reveal: Well, Mariya on Kanako... repeatedly. The latter knows what's beneath his skirt (after all, she grabbed them in episode 1), but still gets sucked in. Then again, so would many viewers...
His sister, on the other hand... let's just say it's no wonder she, like Kanako, Does Not Like Men. And yet, she has to tolerate them because she has to impersonate the saintly exterior of her evil brother (which she manages to pull off because she really is saintly).
Wardrobe Malfunction: Poor Ayari suffered this... twice. Both incidents even happened at the same feast. The first was as a child, when Shizu (then posing as Mariya) stumbled on her and accidentally revealed her panda-print panties. The second was as a teenager, after Mariya saved her from falling off her float. Cue pan-down shot of Ayari's breasts and Kanako staining the statue of the Virgin Mary with her epic nosebleed.
Year Inside, Hour Outside: For failing all of her tests, Kanako was sent by God to... somewhere so she can spend a year studying for everything. She comes back a week later with lampshades abound about how long it felt for her and the various changes that happened in the interim.
Turns out most of the "changes" were set up in some way by Mariya just to mess with Kanako's head, or by sheer misunderstanding.