Otonashi-san has just transferred into a perfectly ordinary high school.
Silent and impassive, she's actually a kunoichi, a female ninja! (Not that she hides it well...)
See what a ninja, the famous traditional Japanese hero, would be like as a high school girl in this off-beat, four-panel manga!
Don't miss Otonashi-san's quirky appeal!!

A happy-go-lucky girl named Silva wielding a scythe and claiming to be part of an evil organization transfers into a normal high school. She befriends her classmates, skirmishes with the heroes of justice, and helps to recruit new members into her organization. It's a comedy full of good and evil, dubious magical girls, hopeless adults, and pudding.

From Badam:

Izumi Koutarou's family have lived in Izumi Hot Spring for generations. But the spring suddenly dried up a couple of years ago, resulting in a huge family debt. As they prepare to skip town to flee from debt collectors, the guardian deity of the house, Konoha-sama, appears. Konoha-sama, (who was supposed to be a really fearsome god), appears instead as a cute girl--wearing no clothes. What will happen to their family debt problem? And what is the power of Konoha-sama?

"Middle Edo Period -- One state becomes the gathering place for sinful martial artists, who believe in nothing other than power, know no other way of life than letting oneself go wild in battle. That state is the Unabara State, the "Haunt of Demons"..."

Washitzu Naosata, the ruler of the powerful state, Unabara, is looking for his successor. He calls upon all 31 of his sons and tells them to search for whoever they believe to be the strongest martial artist of all. Each of their chosen martial artists are then to fight against each other - until only one remains. Whoever is the winner, whoever has the strongest martial artist in the nation by his side, will become his successor...

Out in the midst of the mountains is the doujo of "Oogame Ryuu" (Giant Tortoise Style). There lives Kurogane Gama, the son of the legendary swordsman, Kurogane Jinsuke, who is believed to have killed 1000 martial artists in Unabara. There, one of the sons of Washitzu Naosata, Washitzu Naoshi, arrives in search of the legendary swordsman, only to find that he has been missing for several years. After seeing the battle style of Gama, Naoshi decides to ask Gama to come with him instead. Wanting to become stronger, Gama agrees with his offer, and that marks the beginning of Gama's battle to become the strongest of all...

Apathetic schoolboy Miharu Rokujou is content to meander through life in the sleepy village of Banten. But his quiet existence is shattered when the Grey Wolves of Iga, a powerful ninja clan, attempt to kidnap him in broad daylight. Only then does Miharu discover that the ultimate power of the hidden ninja realm — a power that can do both great good and great harm — is sealed within his body. As battles erupt among rival ninja clans seeking to control him, Miharu must overcome his apathy and learn the ways of the ninja if he wants any shot at survival!

Kaguya is a boy in an all-girls' school for demons [fox spirits, succubi, werewolves, etc]. Being the only human is bad enough, but the added risk of his manhood being discovered makes for silly and unbelievable (deliciously enviable) situations.

Mari Kurusu has had a crush on Kuro Rouzen (the weird guy in her class) for quite a while and when he eats her love letter she thinks it means rejection. Later she finds out his secret, that he is part of a top-secret organization that protects the humans of Earth and he brings her back to the organization to erase her memories. But for some reason, the organization choose's not to erase her memory...

Werewolves, demons, monsters, vampires. All these ferocious creatures are afraid of the same thing: the beautiful Princess Hime, an awesome warrior who fights off the forces of evil with a chainsaw and a smile. Not only does she look great in a tiara, she has power that allows her to raise the dead. She's a girl on a mission, and with the help of her undead servant and a supercute robot, there's no creature of darkness she can't take down!

Kagome is a modern Japanese high-school girl. Never the type to believe in myths and legends, her world view dramatically changes when, one day, she's pulled out of her own time and into another! There, in Japan's ancient past, Kagome discovers more than a few of those dusty old legends are true, and that her destiny is linked to one legendary creature in particular--the dog-like half-demon called Inuyasha! That same trick of fate also ties them both to the Shikon Jewel, or "Jewel of Four Souls." But demons beware...the smallest shard of the Shikon Jewel can give the user unimaginable power.

Won the 47th Shogakukan Manga Award in the Shounen category.

Otokojuku - a private school for juvenile delinquents that were previously expelled from normal schools. At this school, Japanese chivalry is taught through feudal and military fundamentals. Similar to an action film, the classes are overwhelmed by violence. Only those who survive it become true men.

from Renta!

Having lost the Sword of Light in the previous battle, Lina and Gourry continue their journey in search of a replacement weapon. On the way, the two of them meet up with Amelia and Zelgadis in the kingdom of Luvinagard while taunting some pirates. Lina is happy to reunite with her old friends, but appearing before her is Luvinagard's Inspector of the Special Investigative Unit; a man called Wizer. However, Lina is amazed at his unusual behavior...

For fighting and humour fans Jo Pae, a not really sane boy, in our modern days, he wants to become emperor of Korea... His first step when he enters high school is to become the leader of the strongest school there is. No one expecting it, he actually takes down all of the school's yankees. Jo Pae is now the enemy to kill! All rival schools wants his head whatever the means!

Manga adaptation of the game Phantom Brave.

Chroma are bounty hunters for hire that deal with all manner of requests, including monster subjugation. A thirteen-year-old girl named Marona lives on Phantom Isle after losing both of her parents at a young age. Her parents had lost their lives during their jobs as Chroma and now she must become a Chroma to earn money. However, work as a Chroma is difficult and many hold her in disdain as the 'Cursed Girl' because of her ability to talk to and manipulate phantoms.

Thankfully, she's not alone since she has the help of the phantom named Ash, a friend of her parents that had died alongside them in a mission. Marona's parents' dying wish for Ash was to have him protect their daughter. Now Ash does everything he can to help defend Marona from the hardships of the world.

An action comedy about a school for training Yakuza

The sequel to the Shaman King and Shaman King Kang Zeng Bang series. Takes place 10 years after the end of Shaman King Kang Zeng Bang and focuses on the life of Hana in his teenage years.

From MangaHelpers:
Before they enter high school, the boys Meguru and Shou are whining about the fact that neither of them has a girlfriend. A strange, large-breasted woman shows up, claiming that she will fix their problem, and kisses Meguru. This odd occurrence is pushed out of the boys' minds when they meet up with Souko, a friend from elementary school, who is going to be in their high school. She's grown up into a pretty young girl, and it seems like the boys might have a shot with her!
That evening, Meguru realizes that the strange kiss may have had more meaning than he thought: he's turned into a girl! He convinces Shou and his mother of his identity, but no one has any idea how to turn him back. Now he's going to have to learn how to be a girl and let go of his hope of dating his cute childhood friend Souko. What will happen to his hopes for a popular high-school life?

Taken from the Holy Scriptures of the Old Church of Selakiel:
"When the Earth begins to perish, the Messiah will descend from the Heaven on wings of light. Clad in darkness, he will be so little yet he will be so immense surely he shall bring salvation to everyone."

"The four saints shall appear to offer him their assistance. One will give the Messiah courage, one will give the Messiah light, one will give him wings, and one will shield him from his enemies."

Note: Chapters are numbered differently starting on volume 7, since it's a beginning of a new arc

The manga is separated into 3 story arcs with close to none relation with each other's characters.
Volume 01-13: Video Girl Ai
Volume 14-15a: Video Girl Len
Volume 15b: Video Girl - Complete Story (about Video Girl Haruno)

Video Girl Ai [From Viz]:

High-school student Yota Moteuchi is so unpopular that his classmates have given him the nickname "Dateless." So it's no surprise when the love of his life, Moemi, is not interested in Yota but instead is in love with Yota's best friend, Takashi. Yota turns to a video rental shop for comfort, but little did he suspect that the shop was magical and that the cute girl on his rented tape would pop out of the television and try to fix his ruined love life!

Randou Masashi, a self-centered, brash karate star, was the victim of a horrific bus accident that left him comatose, his face terribly disfigured by extensive burns.

Genius plastic surgeon Dr. Manabe saved Randou's life and went to work on his face, gradually reconstructing it based on a photograph found in the wreckage of the bus. But in a cruel twist of fate, the photo that the doctor used as his reference was not a picture of Randou, but of Rina Kurimi, the girl whom Randou has a crush on!

Ten-year-old prodigy Negi Springfield, has just graduated from magic academy, and in order to become a master mage he is sent to Japan to teach English at an all-girls middle school. But Negi has a bigger dream than just becoming a master mage. He wants to find his missing father, "The Thousand Master", the strongest mage that has ever lived. And he soon finds that searching for his father wont be as easy as he first hoped. In fact, it pushes him and his students into life-or-death battles that decides the fate of millions.