Childhood Friend Romance: Mariya, of course. She's loved Mizuho for a long time, but wanted him to grow up a little. When he did, she realized that that's not what she really wanted at all.
Compressed Adaptation: The anime skips over the arc regarding the ghost in the auxiliary music room and Mizuho's teacher. Also, while it follows the Mariya/Takako branching and implies a Takako ending, it actually skips over most of the content exclusive to her route. Finally, little if any content from the other story branches make it into the story.
Conflict Ball: Despite finding out and being okay with it in other routes, when Yukari discovers Mizuho's true sex at the beginning of her route she gets very upset and causes the turn for the dramatic in her story.
Cooking Duel: The swim competition beteen Takako and Mariya.
Flung Clothing: Takako and Mariya fling their clothes when challenging each other for a swim competition.
Fully-Clothed Nudity: Averted. Shion was never embarrassed to change in front of Mizuho not because she didn't like him but because she figures underwear and bathing suits show equal amounts of skin anyway.
Gone Horribly Right: From Mariya's perspective only. She wanted Mizuho to grow to care about people more and he did, at which point she realizes she just wanted him to care about her more.
If It's You, It's Okay: Yukari's confession happens when she still thinks Mizuho is a girl and has decided that she's not a lesbian. But she actually gets pretty upset when she discovers the truth moments later.
I Have No Son: Takako disowns her family in several endings due to really hating them.
Shion has a congenital birth defect that is actually easily operable, but she's slightly nervous about surgery and feels little pressure to get it since even without it she'll probably be fine. At worst, she dies about ten years younger than she would have, but it would be ten years of an arranged marriage.
No Periods, Period: Averted: Mizuho, despite being male, claims to have one to get out of PE class. Shion commiserated and spent several moments going into how hers have rather heavy flow too, before remembering that Mizuho isn't a real girl. He's just THAT good at faking it.
Princely Young Man: Mizuho, before starting to crossdress and pose as an Ojou. Even afterwards, some of the girls talk about his more impressive moments as him acting like a fairy-tale prince. Even the ones that don't know he's a guy.
Puni Plush: In the manga. It makes Mizuho's assertions of manhood less credible than they already are.
Rapunzel Hair: Mizuho always had long hair even back in his childhood. It sure helped with the disguise too.
She Cleans Up Nicely: Kimie gets prettied up at the end of Takako's route to help get the student body to know her beyond the stuffy glasses girl image.
Sins of Our Mothers: Mizuho lives in the room that his late grandfather arranged for him: which is the very same room that belonged to his Missing Mom during her school days and it is also the room where Mrs. Miyanokouji's devoted Ill Girlkohai, Ichiko, died of exhaustion while waiting for her to return. Things ain't that grim, however, as it turns out that said kohai survived as a (rather cheerful) ghost and it is Mizuho's task to make amends to her for his mom's untimely departure 22 years ago.
Genre Savvy: Tsunderella seems to know about the fairy tales she's put in.
Happily Ever After: The story ends with the usual Happily Ever After ending with the prince and Tsunderella together. Then it's subverted when they don't live prince's life, but Tsunderella's, and have to work for the evil step-sisters. And finally double subverted, since they're actually happy anyway.
Magic Mirror: Kei asks her mirror who the most evil one is. She's happy to hear she is.
Noblewoman's Laugh: Takako laughs like this in the beginning of the story. Just after she wonders why she was laughing so much, in a few scenes showing her as extremely accomplished. Then she laughs some more. And is struck by a falling washtub, which causes her to fall off the cliff. Then she's struck by lightning again.
Nose Bleed: Takako's nose bleeds when looking at the prince.
Prehensile Hair: Sion caputures Takako with her hair when she tries to run away.