The twins Maria and Noel have always lived together and are very closely linked. When Maria decides to enter Morinomiya School because of the beautiful eyes of its basketball coach, Noel, who refuses to be separated from his sister, decides to enter the same establishment. Unfortunately, there are no spots left for boys. He thus decides to pass himself off as a girl! But school life is not easy when one must constantly play in a comedy! Especially when Noel rapidly falls in love with Miyu, a fellow classmate, while he himself is courted by another student.

Milk is a young and childish girl living with her aunt in Orange Town. One day, she is told that a guest is coming over to stay with them for a while. Milk's aunt had said that the guest is cute and pretty. Milk, excited about her new friend goes to meet the guest at the fountain. Milk's childhood friend Vitamin and others accompany her at this time. Through an unforseen event, Milk arrives late at the fountain with the guest nowhere to be seen. They did however, find a handsome young boy asking for directions to Orange Town.

Oneshot from Kimi ga Iru Shinya 2-ji 20-pun

An antisocial salaryman who becomes obsessed with an elegant hunk he sees at the lunch cafe.

From VIZ:

Seiji Sawamura is the toughest seventeen-year-old in town, feared by all for his fighting prowess and his deadly "devil's right hand." But at heart, Seiji is a softy, and all he wants is an end to his seventeen-year history of being a lonely single guy. Unfortunately his tough-guy reputation only serves to decrease his popularity with the ladies. But what happens when one day, his right hand becomes a girl?!

Everyone lies when they are young, but the lie Kobayashi Hiro told when he was just six haunts him daily to this day. He claimed that he was abducted by aliens, and, even though it was quickly discovered it was a hoax, thanks to national attention, the town became a hotspot and tourist stop for UFO fanatics.

So when the beautiful Yamada Meteor transfers to Hiro’s school, claiming that she is an alien and Hiro is the only one that can save the planet from destruction, he thinks that the whole thing’s a prank. He quickly learns that she isn’t joking.

Meteor is here to test if humanity is worth saving from the monstrous asteroids headed toward Earth. To prove humanity’s worth to the universe, Hiro must complete the assigned missions, even if they are a little perverted.

Blogger, Shio, meets up with some friends he met online through his blog. He is going to meet Miya (supposedly female), a blogger he hasn't met yet. He is surprised to find out that Miya is a very tall man who has a very calming effect on others.

Thirty years ago a series of meteorites rained down on Earth, destroying much of civilization. Decades later, pockets of humanity are beginning to reemerge, but many of the children who have been born after the crisis have been mutated by radiation from the meteorites. They are called the Meteorite Breed.

Tooi, a fourteen years old kid that eats a lot, is one of the Meteorite Breed. But he is a rare one...

From Shoujo Crusade:

A boy who only loves black and a girl who enjoys all the colors. What will happen when they clash?

Satomi High's Football Club members are bunch of weirdos, there's a former yankee (delinquent), a former Hikikamori, one short-tempered guy and on top of that their captain is a 'chibi' (shorty), who looks more like primary schooler than a 2nd year high schooler, but don't be fooled - despite the fact of being all-freshman brand new team in a brand new high school, those guys made it to the best 4 of Chiba Prefecture last year! Their newest recruit is an almost 2m high guy, who is surprisingly bad at headings (despite having a height advantage). Fortunately the chibi-captain notices his potential as an attacking midfielder... How far can this team possibly go in this year's tournament? (From:MyAnimelist.net)

Masakichi-kun is a first year high schooler working as an errand boy for the upperclassmen bullies. One day he slams into a female member of a biker gang, touching her breasts... She saves him from a falling steel frame from a construction yard and leaves without saying anything... Later on, she suddenly shows up at his school causing a ruckus. What will happen to Masakichi-kun?

Kogane is a socially clueless, glasses-wearing girl who works at a convenience store. She has a huge crush on her manager, Fuuta, but he doesn't seem to return her feelings at all. Luckily, Kogane has a little sister, Akane, who is much more fashion conscious and adept at social situations. Akane is determined to help her awkward big sister get the boy she wants!

From Aerandria Scans:
“Cause trouble in Shibuya, and I’ll hear everything.”
Chiryu Mamoru is the former Shibuya Gang King (Crime Boss). Now he’s protecting the streets of Shibuya as the youngest lawyer in history. With an ear piercing as his lawyer badge and law as his weapon, he works to destroy the nest of evil and to protect the people. Introducing one lawyer’s all consuming fight against heresy!
“You can’t protect anything with violence… that’s why I choose the law!”

The story revolves around Takumi Tsuzuki, a boy who lives with his older "sister" Otome, although the two have no blood ties between them. Otome manages a run-down confectionery store called Stray Cats. One day, Otome picks up a mysterious beautiful girl off the streets.

Mato-chan is a 3rd grade elementary school girl that likes bugs sooo much. Take a look at Mato-chan and friends' daily life!

Mikio teases his neighbor Mariko a flat-chest and she calls him a midget. When one day Mikio turned miniature and ended up in Mariko's care, they discover how wrong they are about each other.

A collection of one-shots:

Vol 1:
Magician
Fairy Tale
Cocona
Plue's Adventures Pt. II

Vol 2:
Bad Boys Song
Magic Party
Christmas Hearts
Fighting Group Mixture

From Intercross:

Hatsune is a useless, devious girl. One day, Hatsune's father decides to make her live with a fastidious boy! Kaede-kun, being fed up with how unladylike Hatsune is, decides to become her tutor.

A sea prince wishes to have Christmas under the sea. Can his butler make his dream come true?

Tomo Fukuya loves taking pictures of himself while cross-dressing, and he's gained some notoriety among his schoolmates because of it. He participates in his school's beauty contest during the school festival against his friend Kei Okabe.

• Nante Zurui Otoko (What a Sly Guy)
Yoshino Nene is a 16-year-old girl who fell in love at first sight with Fukazu-san, a man 9 years older than her. She sends him emails, trespasses (?), and intensely hits on him, but he won't respond to her. Finally, he told her: "I won't ever fall in love". But he looked very sad when he said that. Nene wants to know his real intentions...
- Intercross

• Kimi ni Makasenasai!
After confessing to someone and being rejected, the infamous girly second year, Kaji-senpai who witnessed the whole thing offers to pick Tajima Rika up. And so begins Rika's transformation into a cute girl through Kaji-senpai's hands.

• Come to My Side
Uchino Tomaki, a 17 year old girl, becomes interested in her younger brother's friend, Shun.

• Kimi wo Itadaki!
About a girl who cannot stop feeling the need to compete with her childhood friend. Her uneasy feeling has made her never thought anything other than competing. Then a confession comes for her.

• Wolf Cherry
A girl bumps into a classmate and finds out his secret... He's a shoujo mangaka!