Another: The fact that his aunt Reiko and his assistant homeroom teacher Ms. Mikami are the same person is not a secret to the protagonist Kouichi, but the anime hides it from the audience until the final episode, making it harder to connect the dots leading to the identity of the Dead All Along person in his homeroom class.
When Ayakashi Triangle introduces Soga's sister Haya, she pretends she's her brother turned into a girl like Matsuri was. This audience is led to believe this is true by starting the chapter as Soga and Ponosuke are attacked by an unseen assailant, then cutting to Ponosuke claiming Haya is Soga. Later it turns out Soga was Mugged for Disguise and Ponosuke was threatened into supporting the ruse.
ef: A Tale Of Memories pulled an awesome example, revealed in the second season of the anime and at the very end of the original game. Hiro, Miyako, and Yuuko are not in the same city as Renji, Chihiro, and Yuu. The two cities are both named Otowa, both have churches and schools. But one is located in Japan, the other is located in Australia.
Getter Robo Devolution eventually reveals that the whole setting is actually a virtual world, a simulation that the Getter Team had started running after their battles against the Hundred Demon Empire. All of Ryoma, Hayato's, and Musashi's trials had been meant to gather data to create the ultimate Getter.
Goodbye, Eri: The fact that Yuta's mother was a verbally and physically abusive mother and wife was obviously well known by Yuta and his father, which were her victims, but was deliberately kept away from the reader, since they only meet the version of her that is shown in the overly idealized documentary. It is not until his father reveals that he recorded the final moments of his mother that the reader sees that she spent most of her time berating her son for being useless to her.
i tell c opens with the news of the murder of an actress at the hands of a stalker, while her actor friend is also stalked by a mysterious woman who may or may not be the actress's murderer. As it turns out, the actor is the murderer, and his stalker is a police detective who is employing the same stalking technique to find evidence of the actor's guilt.
Magical Girl Lyrical Nanoha StrikerS had Subaru and Ginga being Combat Cyborgs. Everyone knew from the beginning with the exception of Erio, Caro, and possibly a few minor members of Riot Force Six (yes, even the antagonists knew).
One Piece has the revelation that Portgas D. Ace is not Luffy's biological brother, but actually the son of the Pirate King, Gold Roger. While this is treated as a heart-stopping revelation by both the audience and most of the One Piece world (and rightfully so), those closest to him were perfectly aware of it and honestly didn't care. Hell, Luffy knew about it ever since they first met, and the only reason he never told anyone is that nobody bothered to ask.
Zekkyou Gakkyuu has several chapters that end up with these surprises.
The Land Of Mirrors has the protagonist think that the land inside of mirrors is real and humans are being replaced by their reflections, the only noticeable difference being that their appearance is, well, mirror-reversed. The real revelation is that the land of mirrors does exist...but that it is our 'real world' that is the mirrored land and our reflections are the actual real world.
Graduate Number 108 has Rina portrayed as an absolute ace student and friendly to everyone, even the residential loner Reiko. The story makes no secret of the fact that Rina has something to do with Reiko's disappearance. The revelation occurs when a flashback shows that Rina is nothing but a self-absorbed bully, who attacked Reiko for calling her out on her fake personality.
The Family Of Five has the strange occurrence of the youngest daughter always being with her family: her father, mother, brother, and sister. Yet nobody ever thought it was a strange thing, not even that the whole family was going to school with her! Sick and tired of this, especially when a crush of hers confesses and realizing she'll never be left alone by them, she starts brandishing a knife...We suddenly cut to a home economics classroom, where a student accidentally cut her smallest finger off. The family of five was actually a 'family' of fingers on one hand.
Bloody Valentine has a yandere stalk Naoyuki's girlfriend and sending her death threats and demanding she stay away from him, with Naoyuki also keeping his actual relationship status a secret from others. The real revelation comes from the fact that the protagonist, Misaki, was the yandere and not the girlfriend.
The Boyfriend Story has Mei learn that a cellphone game labelled Boyfriend Story is really popular, and allows the player to create their perfect boyfriend in terms of appearance and personality. The boyfriend is an Artificial Human, barely distinguishable from regular humans. Mei proceeds to ignore her best friend in favor of cuddling with her boyfriend, until she learns that he's a yandere and she deletes him. As Mei rushes to her friend's side to apologize, Mei disappears. She was also an Artificial Human created by her friend from a Friend Story cellphone game. And a throwaway line near the end points out that a good half of the humans walking around are artificial ones.
