Special Extra Story of One Piece 

"Long, long time ago... God descended down to the world engulfed in darkness. With the threads made from sheep's wool, He created one wondrous piece of cloth, gave rise to another world. That world is known as 'Divine Cloth'." This is the legend that was told from generation to generation.

Beneath the Earth of Divine Cloth is the world engulfed in darkness. There lives the creatures that were sealed by God known as Bugs. Frequently, Bugs plunge out from their world, creating holes on Divine Cloth. To fix these holes and reseal the Bugs beneath the ground, a young man and woman, Ryle and Marino, set out on their journey.

New dawn of historical gunfights! A Meiji Era like no one has ever seen before is here!

In a world where monsters called Yoma prey on humans and live among them in disguise, humanity's only hope is a new breed of warrior known as Claymores. Half human, half monster, these silver-eyed slayers possess supernatural strength, but are condemned to fight their savage impulses or lose their humanity completely.

Clannad is set in a high-school located in a Japanese town. Tomoya Okazaki is a third-year student who doesn't take his studies seriously. Always late for class, he's seen as a delinquent by the rest of his classmates who are busy preparing for their entrance examinations. Needless to say, he doesn't have too many close friends either.

Tomoya seems not to mind too--until he meets a few other girls from his school. Though he doesn't care much about them at first, he soon opens his heart to them as they get to know each other better.

Clannad is a romantic youth drama that's likely to be more down-to-earth than Key's other works. But like Kanon and Air, Clannad's story is expected to be another touching and heart-breaking weeper.

Based off the game of the same name.

The mighty Kingdom of Goguryeo is in the midst of a war which has raged on for decades. In need of talented warriors to help lead their people, O'Rhang Yhun is sent on a mission by his master into enemy territory to find and bring back his eldest brother. However, just as O'Rhang departs on his mission, his master, a renown warrior and general of Goguryeo, passes away. Unfortunately for O'Rhang, his 2nd eldest brother has always been jealous of his martial arts potential and betrays O'Rhang by branding him as a traitor defecting to the enemy. Having been branded a traitor, he is pursued and nearly killed. As fate would have it though, O'Rhang is able to escape from his homeland barely managing to survive when a maiden as beautiful and graceful as an angel saves his life. Join O'Rhang Yhun in this action packed adventure-love story to uncover the secret behind the martial arts his master passed onto him (Sa Shin Mu), his quest to find his oldest brother, and the score he has to settle with his 2nd eldest brother! [The Continuation of this manhwa is the manhwa NOW.]

In this school fantasy story set in the distant future, creatures contaminated by pollution have overtaken the land, forcing humanity to live in isolated mobile cities called Regios. One such city named Zuellni is a self-contained school in which freshman Layfon Alseif has just enrolled. Layfon reluctantly joins the 17th Martial Arts Studies Unit led by the third-year student Nina Antalk and embarks on a series of adventures.

This version recounts a slightly different version of Layfon's story.

From Potato-Land:

A girl named Nagisa Akira, is said to be the reincarnation of the Virgin Mary aka Maria's Daughter. The Vatican, realizing this, has sent one of its elite agents, Takagi Chrome, code named “Crimzon” to protect her. Chrome is one of the elite assassins directly under the control of the Vatican, used to carry out terrorist acts and the assassination of world leaders. Chrome's new mission is to protect Akira so that she does not fall under the hands of the Protestant English. Thus begins the journey to protect Maria’s Daughter, and to find out about Chrome’s mysterious demonic power.

From Tokyopop:
The plot centers on Kazuki Sendo, whose passion and talent for painting and drawing propels him into the world of doujinshi (underground comics). Soon, Kazuki's everyday life is consumed by the fanboy life and his girlfriend is beginning to have some serious doubts about him...
Sure, his new career as a struggling artist has begun, but at what cost to his friends and family?

The story takes place in the same official Code Geass history as the anime, but in a different era. The title character, Renya, is a 17-year-old boy with a mechanical left arm and shuriken throwing stars as his weapons of choice. The story begins when Renya encounters a mysterious, perpetually young witch named "Reifuu C.C." C.C. has appeared in Japan's historical Edo era to seek a new partner for a covenant. Meanwhile, a mysterious man, with a striking resemblance to the character Lelouch of the original anime, also appears with unknown intentions.

An alternate Code Geass story in which Lelouch's fate is unknown after his meeting with C.C., whether he be dead or alive. Nunnally makes a Geass contract and gains the power to read the lines of the future. She also obtains a new body and takes up piloting an unusual Knightmare Frame.

A Demon wants to turn into a human because she fell in love. This is the story of her turning into a human, with, a slightly realistic view as to what might happen..... Well, only if demons were real to begin with.

One day, when Hidaka Kishi is going to school with his close friend Kimiko, he notices a strange new song on his music player: "Who Killed Cock Robin?" Little does he know, a murderous game is beginning, with him as the target--the Cock Robin. Fourteen other players (called 'birds') are all competing to kill him, in exchange for making their wishes come true. However, one of the birds, Saedano Minami, seems to have other plans. To Hidaka's confusion, she decides to protect him, but what is her ultimate goal? How will Hidaka survive this deadly game?

From Viz:
A contagious Monster Flu is spreading around town like wildfire. Can the town's troublemaker and his friends get the medicine in time to save everyone?!
Paifu, a half-vampire half-werekoala, is always getting into trouble. With his trusty sidekick, Jose the ghost, he's out stealing watermelons, befriending murderers and causing a ruckus. But not everything is fun and games when the contagious Monster Flu sweeps through town. If the sick monsters don't get some medicine within a month, everyone will die! But only the one who has the medicine is the Witch who lives high atop Horned-Owl Mountain...750 miles away! With the help of a former sumo wrestler, Paifu, Jose and tagalong Arpon are off on an adventure! But, will they get the medicine in time or will they become victims themselves?!

With their school shutting down for good, the students of a small town were heading for different directions in life. For Minase Tamaki, who was staying in town to find a job, it might be the last time she sees her crush Shindo Yuuma, who is moving to the city to attend a new school. She asks him to do a little prayer that is supposed to help people cross paths again even if they become separated. But her classmate, Yuzuki Erina, overhears their conversation and, out of jealousy, decides to ruin her plans by inviting their entire class on what was supposed to be an intimate spell. As soon as the charm goes off, the ground splits in half, swallowing the entire class and, when they wake up, they find themselves in an old school campus. Unable to find a way out, they wander the corridors, trying to figure out where they are. But it seems that the building isn’t as abandoned as they thought it was and, in fact, something evil is lurking in the shadows.

Asahi and her friend Yamato went together to an exclusive event as test players for a new game from the cellphone-game company "Sky Nova." The test players were a diverse lot of all ages, from ordinary teens like Asahi to popular idols. The company took all of them on a cruise to explain the rules of this island-based, treasure-hunting survival game. Suddenly, during the presentation, all of the participants lost consciousness. They woke up on an actual island wearing a strange watch with the words "Game Start." Now they are all stuck in this survival game, which has become all too real and deadly!

Kentaro was a normal teenager in school in the country of Kenko, but when the neighboring kingdom of Sigma launches a surprise attack, he learns a secret about himself. Sigma warriors head for the Giria Academy where Kentaro attends in order to assassinate him. He and his classmates are saved by the Sanjuki, three of the most powerful and famous knights of Kenko: Tsubasa Sho Tenkuin, Shingo Go Daireiji and Kyonosukezaemon Dan Kuronokuzu. Kentaro learns from the Sanjuki that he is the heir to the throne of the kingdom of Kenko and his life will never be simple or normal ever again!

The series consists primarily of short vignettes detailing the adventures of the Crossbone Vanguard space pirates three years after the original manga.
The first story is set during the One Year War and deals with a young Umon Samon. The series also features the "return" of Grey Stoke, an aged Judau Ashta under an alias, who first appeared in Hasegawa's Mobile Suit Victory Gundam Side Story manga.

From Snow Kiss Scanlations:

Towa became a sweeper admiring the legendary sweeper called, “Orange-Eyed Messiah”. The task of sweeper, which requires to “sweep” the monsters Adys is quite hazardous. On his first real attempt at fighting Adys, Towa encountered Kei, a former sweeper who saved him from being killed.
Towa asked Kei to take him as a student. However, not only Kei plainly rejects Towa’s request, he tells Towa that he saw the “Orange-eyed Messiah” die!? An appearance by a mysterious man who seems to be connected to Kei showed up with a grudge from the past. Who is he and what is his relationship with the “Orange-Eyed Messiah”? Will Towa finds out about Kei’s past too?

Spin-Off of CRIMSONS - Akai Koukaishatachi