The Seven Mysteries

Apparently, mysterious phenomena come in groups of seven.

Why? Well, that's a mystery. There's probably six more.

Especially common in a school setting, these tend to be awkwardly brought up during summer episodes, where mysterious legends are attributed to a not-particularly-old place. Nearly always end up being complete horsehockey, except for the Cute Ghost Girl. Common themes include voices in an empty room, faces in a wall, staircases with more steps going up than coming down, and other variously spooky and paranormal things.

Note that this is not the same as there being seven Objects of Power, or other Numerological Motifs associated with the number seven - it's specifically the Japanese cultural phenomenon of places with seven unrelated but strange and mysterious things that happen in an otherwise normal place.

A common punchline is for the seventh mystery to be that there is only six mysteries.

Anime and Manga
"Ken: Once upon a time there was a little maid called Kurimu who served her master with all her heart and all her body and all her soul. The end. Kurimu: NOOOOO!"
 * In Urusei Yatsura, the teacher Onsen-Mark tries to do the traditional midsummer spook-the-youngsters-with-scary-stories routine and mentions the Seven Mysteries of Tomobiki High. Unfortunately, due to the weirdness magnets in the class (Moroboshi and Co.), most of these were already the subject of various previous chapters, and the class was bored.
 * The girls in Strawberry Panic do a similar investigation.
 * Came up in Mahoromatic, with the added twist there actually was a ghost in a classroom.
 * "The Seven Mysteries of Fudo High" in Kindaichi Case Files.
 * Mai's arrival at Fuuka Gakuen in Mai-HiME quickly becomes one of that school's seven mysteries.
 * Appeared in the later seasons of Ranma ½, revolving around a "lost school store" and its aged keeper, "the Secret Don of Furinkan High" whose stories of the school's past tied into the Warring States era, WWII, the Mongol Empire, and the Napoleonic Wars (and were, of course, pure fabrication). A later episode introduced an actual ghost girl to haunt the place.
 * In Mythical Detective Loki Ragnarok, the girl sidekick takes Loki to her school to show him their seven mysteries. As usual, only the last one lacks a mundane explation.
 * In the Toei Animation version of Kanon, after discovering Mai fighting demons at the school, Yuuichi asks Kaori if she's heard of a girl that appears at night. Kaori thinks he's talking about the obligatory "cute girl ghost" of the seven mysteries. However, every single one is completely bogus, including the ghost; Mai's supernatural connections have a very different origin.
 * One of The Seven Mysteries is the main cause of plot in Uta Kata. The rest don't show up.
 * Dirty Pair Flash manages to set up a High School AU situation in its second season as an excuse for this plot.
 * The third episode of Otogi Juushi Akazukin revolves around the seven mysteries. They all turn out to be caused by the heroine, Akazukin.
 * There are Seven Mysteries within Green Dolphin Prison in JoJo's Bizarre Adventure : Stone Ocean - one of them being the unusual and rare appearance of Louis Vuitton bags at the prison shop - however, they don't appear to have anything to do with the plot and are the least mysterious things about the dangerous prison.
 * The school in Kekkaishi has 77 Mysteries. The increase is due to the school sitting on the manga's resident Applied Phlebotinum.
 * One episode of Maria Holic focuses on the seven mysteries of Ame no Kisaki Girls' School, a high percentage of them involving blood. To the surprise of no one, Kanako is directly responsible for all of them due to her fantasies. Kanako's homeroom teacher later tells her that the seven mysteries applying to the whole school change every year, but seven other mysteries about Kanako's dorm manager have never changed; they range from the genuinely mysterious ("what the hell is her real age?") to mundane Fridge Logic ("why are Virtual Boys not banned along with the other electronics?"). If anyone happens to learn all seven mysteries, the dorm manager will do...well, something, anyway.
 * Ikki's school in Air Gear has seven mysteries, most of which are explained by the presence of a secret room Kogarasumaru eventually uses as their home base.
 * Seitokai no Ichizon - Manga - The students confuse this with a scary story tournament, so the school ends up with dozens of mysteries, all horrifying. Minatsu undoes it all by adding the legend of the girl who goes around destroying all the ghosts. But Ken's story is the scariest:


 * Higanbana no Saku Yoru ni is all about a school's seven mysteries (and the creation of an eighth...)
 * A major plot point Tasogare Otome X Amnesia. The Paranormal Club believes that finding all seven mysteries will help them discover the secrets behind Yuuko's murder. Much of the plot involves distinguishing between rumors or ghost stories and true mysteries.
 * One episode of the Keroro Gunsou anime has Keroro setting up shop in an abandoned school, planning on staging a few ghost sightings and turning it into a tourist trap to help fund the invasion. He tests out his scheme on Fuyuki and Momoka, who happen to be in the same building on a ghost-hunting expedition, by throwing a set of seven (actually five) "school haunting" cliches at them.

Radio Drama

 * The plot of the Hatoful Boyfriend Drama CD is about Ryouta and Sakuya investigating the seven mysteries of St PigeoNation's.

Video Games

 * In Kingdom Hearts II, part of the extended prologue in Twilight Town features Roxas and his friends investigating "Seven Wonders" that appear to have mundane explanations, while the true explanations are quite extraordinary, the blanket explanation being that they're either glitches in the simulation or Nobodies screwing around with things on purpose... Well, except for the staircase one. Rai's an idiot. The Seven Wonders are also in the real Twilight Town in 358/2 Days, and inspecting Pence's notes reveals that they're all the same as the simulated Twilight Town's with similar mundane explanations, with the exception of an "Eighth Wonder," which turns out to be an invisible Heartless.
 * In Paper Mario: The Thousand-Year Door, the Glitz Pit has its Seven Wonders that one of the NPCs tell you. It turns out that they are all true, and you must investigate them to advance the plot. Of course, in typical Mario fashion, these Seven Wonders have some humorous explanations and aren't all that mysterious given what Mario has seen in the past.
 * A mission late in Crisis Core has Zack seeking out the seven wonders of Nibelheim, all of which have mundane explanations, and gets him a reward for figuring out.
 * The third Mega Man Star Force game has "The Seven Wonders of Echo Ridge," despite there being only six, as mentioned by an NPC very late in the game, after no doubt having driven batty many players who thought to look for them all out of curiosity.
 * Apparently, the Seven Mysteries of North High are the subject for Suzumiya Haruhi no Chokuretsu, a game released for the DS in Japan.
 * In the second Blaz Blue Carl's Gag Reel has him recall the time he, Noel, Tsubaki and Makoto (who he was at the academy with) had him go through one of these because he was feeling homesick.
 * In Da Capo II, these mysteries are the basis for a Test of Courage.
 * In Yakuza 3, a series of subquests in Downtown Ryuugi centers around 'The Seven Mysteries of Ryuugi', as told by a group of gossiping schoolgirls. Inevitably, each of the mysteries turn out to either have a mundane explanation, or - more frequently - comes down to somebody running a scam. For the perfect punchline, the main character himself essentially turns into the Seventh Mystery - a 'ripped older guy' who shows up when people fall prey to loansharks or scammers to beat them up. Considering how invincibly Badass Kazuma Kiryuu is, he's certainly closer to being supernatural than any of the other so-called mysteries...