Hiromi can't wait for her cousin Makoto to come live with her - but when "he" finally shows up, she gets a good deal more than she bargained for. Toshiki Yui turns a hentai fetish into the plot hook of this high school situation comedy.

From Storm in Heaven:

Welcome to Momoko's waking nightmare. Things were settled, they were! She was SUPPOSED to have gone to a normal school, made normal friends, and led a blissfully normal life. But the universe is just cruelly, irredeemably, monstrously unfair, so instead she found herself thrown out of home, stuck in an all-boys boarding school with a roommate she hates, cursed with a hideous haircut and wearing clothes which, to be frank, she wouldn't be seen dead in. And the only thing worse than her current situation is the one that she'll be in if anyone ever realizes that she is, in fact, a girl. Everything is wrong! Particularly the fact that, even though she's surrounded by amazingly gorgeous guys, her chances of romance are less than zero. But with life this complicated, something's bound to give - and so it does.

Handsome, tall, and charming bachelor Fin Deitory that every woman wanted just made the most regretfully and stupidest mistake of his life. It also changed his whole career which he imagined to be an awesome agent in the SDF, abbreviated for Special Dispatch Force. On the day he was supposed to be starting his job though, he enters the wrong room mistaking the plate name sign to be "SDF: Special Dispatch Force" but instead, it was "SDF: Special Doll Force". He learns that the group was a secret to the real SDF and was only consists of doll collectors. But the handsome people trap him there because he was also handsome making him also a doll collector. Being a little bit conceited and such, Fin can't think of himself as a doll collector but he later realizes the importance of it..... From Baka-Updates: Fen has just been assigned a position in the Special Dispatch Force (a.k.a. the "SDF") protecting the King of Vera Morgan. When he arrives at the office for the SDF he discovers he's been accidentally enrolled in the Special Doll Force instead! Fen discovers to his dismay that his new job is to search out and retrieve "bran dolls" with the help of four strange but beautiful men - who have more than just the job on their minds!

Hayashi Shoutaro is an otaku and a student who sucks at studying, the results showing on every test. And if that wasn't bad enough, he also calls out things like, the one who scores the lowest has to clean the classroom by themselves. In his class, there is a girl he likes, Kanda Yayoi, who always gets top scores and is popular among the whole class.

When he arrives home after cleaning the classroom, he's met by his perverted, otaku sister who has him cross-play (cross-dressing cosplay) to go to an anime merchandise display. There he meets Yayoi, who it turns out is also an otaku, and she falls in love with his cosplay persona...?

From Tokyopop:

A rude girl and an effeminate boy switch bodies and find that it might be a better fit for both of them in this crazy comedy:

Nanako Momoi is the belle of high school... as long as she stays quiet. Once she shows her true self, guys' dreams are shattered for she is a true tomboy. Akira Uehara has the looks and brains, but, unfortunately, his personality is so dull it overcasts a shadow, and nobody notices him.

One day, Nanako's grandfather comes up with a crazy invention, and Nanako and Akira trade bodies! She's in his body, and he's in hers!

From MiiRache:

In the land of Carat, a battle for the queen’s throne and the prince’s hand in marriage is up and coming. Yuni and Melissa are chosen as candidates for the throne and until a winner is determined, the prince remains in a magical sleep. But what does this have to do with Baba Kanon, a simple ninth grader with thoughts of revolutionizing herself?

A series of unrelated short stories about sisters with brother complexes (and in some cases, the brothers also have sister complexes).

From Tokyopop:

Naka is an aspiring young model with a problem: her face tenses up into a terrifying spectacle whenever she gets nervous on photo shoots! Naka's rival is Umi, the hottest model at their agency. But Naka soon discovers Umi's secret--and hilarity ensues behind the cameras!

The story revolves around a convenience store Paraiso. The store was once very successful and attracted quite a crowd because of its unique employees, but suddenly, various weird mishaps started happening one after another in the store, making it lose its popularity and making the customers believe it's cursed. A fresh college graduate, Ichinotani Hikaru, going to a job interview, somehow ends up getting forced into a job in this store. What kind of fate awaits him now?

Sumi is in love with Mitsuru, but he doesn't seem to be interested in her as a woman. Determined to look more sexy and mature, Sumi takes an experimental growth hormone that her scientist father has been developing. However, the medicine backfires. Instead of changing into a buxom femme fatale, Sumi changes into a beautiful young man! She--he--is so gorgeous and so cool that even Mitsuru begins to take notice. Although the new situation with Mitsuru is imperfect, Sumi discovers that she can be closer to her crush: they can talk man-to-man. Yet, being Mitsuru's friend also has a downside, particularly when he reveals that he is in love with a girl in his grade!

Yuuki Ashikaga is a high-school freshman at Sakakino Academy. While working as a student librarian, he grows enamored of Kotonoha Katsura, a girl who frequents the library. Unfortunately, Kotonoha is already dating Makoto Itou, another schoolmate.

The situation is further complicated when Chie, Yuuki's older sister introduces him to Roka Kitsuregawa, her kouhai in the basketball club. Roka becomes interested in Yuuki, who only has eyes for Kotonoha. In order to make him jealous, Roka lies and claims she already has a boyfriend, her former classmate Makoto Itou. Unfortunately for all of them, Roka's lie sets off a chain of events no one could have predicted...

Note: Cross Days takes place in the middle of the original School Days storyline and provides an alternate take on how things might have turned out.

From Intercross:

For all of Mao's life, she has longed to be girly and have tea parties with beautiful girlfriends. And finally, she has that dream right in her reach, until she walks in on three boys changing at her private all girls school... What's a girl to do when another girl she admired turns out to be a guy?!

From Shoujo Crusade:

Karin HATES guys. She can't stand the sight of them, let alone be near them. But after a near death experience she finds herself waking up to a guy she doesn't know, within a guy school and in a guy's body!!?!

Jeong-Hwan received a letter from his sister Ji-Yeong that said, "Please rescue me, the devil is here!"

His sister goes to an all-girls school and in order to rescue her, he must disguise himself as a female student. In this school, all students are candidates to become "the bride of the devil."

Just before entering the university, Yanagiba Masahiko's father died in a car accident. His mother died when he was four, which makes him now really an orphan. But even before the death of his father, he didn't have a family life, as his father was always busy or abroad.

When his mother's younger brother and his wife decide to invite him to live with their family, his life takes a turn. But it is not going to be the normal family life he is imagining for himself. What is the "terrible" secret that led his parents to break the bonds with his aunt and uncle? What could be the true nature of his cousin, Shion? And last but not least, will this "terrible" secret eventually get Yanagiba, too?

Becoming part of a family...

Bohm (meaning spring in Korean), on his way to give his dad, Detective Ghim, (who's been working for 10 days straight) some underpants at the police station, sees a girl by a vending machine and wishes to see her again...

Mahnsoo, a boy with a strange lonely past, the only witness to an important criminal case, must undergo a disguise as a girl and stay together with Detective Ghim's family until the investigation is over and the case ends. So he meets Bohm again, and trying to get close to his new icy brother is not easy...

From Wikipedia:

Shimeru Futaba is a normal high schooler living a normal life, active in his school's wrestling club and slowly getting closer to his awkward love interest, Misaki. This fails to last, as he discovers his family's hereditary genetic defect that becomes active at adolescence. Although it will eventually become controllable, excitement and stress now make Futaba switch sex. Hilarity ensues.

From Viz:
Miaka Yuuki is an ordinary junior-high student who is suddenly whisked away into the world of a book, "The Universe of th Four Gods". There she becomes the priestess of the god Suzaku, and is charged with finding all seven of her Celestial-Warrior protectors.

A Japanese student named Arisu gets on the wrong bus and winds up in some sort of homoerotic version of Lewis Carroll's Wonderland. The last thing you want to do in a land where people change shapes at the drop of a hat is to drop the soap and introduce yourself as Arisu (identical in Japanese to Alice), lest you start looking like one! And Arisu does, slowly but surely...

From Ivyscan:

Karin and Lisette are witches who trained together when they were younger. After a long absence, Lisette has moved to a nearby forest and seems to be stealing Karin’s customers. Karin really wants to see her old friend again, but she can’t seem to get past Lisette’s apprentice, a young man named Ruin…

Volume 1 Oneshot: Meeting Place
About a student that can't say thanks to her overly enthusiastic teacher; so, she is thrown back in time to figure out that she still can.

Volume 2 Oneshot: Mission Sachiyama
About an after school program that trains modern day ninjas.