A high-tech adventure set in a digital world. Sam Flynn, when he was a child, has been told stories about a different world his father created. After 25 years of not seeing seeing his father, he enters his dad's arcade and finds himself pulled into the digital world of "TRON" where his father has been trapped and living for years. This is a life-and-death journey of an escape across a cyber universe that has become far more advanced and exceedingly dangerous.

Based on a movie

From Mango Scans:

The world is completely changed when “Sacred King”, the military satellite created by the scientist Arthur, loses control. Arthur’s personal army, the “Trance Knights” have broken up, and other organisations are attempting to take control of the satellite. In the midst of these events, Arthur’s daughter Ley, who holds the key to the “Sacred King”, encounters Gawain, one of Arthur’s former knights.

One of the manga that take place in the Touhou series (mainly known for the games by Team Shanghai Alice)

Based on a novel by Wada Ryou, Shinobi no Kuni brings a story that blends history and fiction as it shows the struggles happening during the 16th century in Iga, a region famous by the Iga Shinobi, the Dragonborns.

From Infinity Studios: Having been born in a secret government laboratory that cultivated esper (telepathic) powers within humans, Shuuichi and two sisters, Sumire and Katsumi, are forced to endure a difficult life as test subjects until their escape. Years later, these siblings are still being sought after by unknown organizations that are after Shuuichi powers as he is what they refer to as the “zero-sample” with the ability to cause “zero-shock.” Scanlated by Helz0ne http://helz0ne.zone-anime.com

Junko Tachibana, a manager of the baseball club of Wakaba High School, is the Madonna of the team. Sawamura, her first love, is an ace batter.Happy and sound love story.

*Included in Aa! Seishun no Koushien

From Tokyopop:

Chiyoharu used to be the leader of the troublemakers, until one day an innocent prank results in a major fire at the school. When his three cohorts take the blame and are expelled, Chiyoharu tries to go on with his mundane life, beating himself up with guilt. Then he meets the mysterious, muscle-man Souza of the North Wind and a ditzy self-proclaimed detective who are trying to solve the mystery behind Souza's amnesia...It's nonstop comedy and action from there!

In a post-apocalyptic world covered with water, Wadatsumi, a person who lives in what appears to be the last piece of land, finds a mysterious girl dragged by the waves of the sea. Where does she come from? Are there other lands in this world?

From Taruby:
After 'The Great Sinking,' civilization on Earth crumbled as the world was drowned in the ocean. One tiny band of survivors eke out a living atop the ruined remains of a skyscraper. Wadatsumi, a young tomboy, is saddled with the care of four elderly gentlemen, until a chance encounter with a group of pirates and a mysterious woman turn her world upside-down.

High-school student Kisaragi Maki has one dream: to be a normal wife. She’s part of a Yakuza family known as Group Kisaragi and her father is the third generation of the group - and he wants Maki to be the fourth generation! But Maki isn’t a ‘normal high school student’. She has a split personality which gets her into all sorts of trouble. Can Maki achieve her dream of being a ‘normal wife’?

A Spin-off of Hitman Reborn.

A girl follows the tradition of her family by testing to be a demon cleaner. During her test a vampire escapes and bites her. In order to reverse the effects of the bite her older brother and said vampire have to go on a demon cleaning job together.

Story about friendship and truth, with of course, a supernatural box.
Begins in a middle school where a mysterious box appears before some boys.

A high-school student named Yu Komori is bitten by a radioactive spider, which gave him spider-like powers. Yu faces Japanese versions of villains such as Electro, the Lizard and the Kangaroo. Yu also has an Aunt May (her name is "Mei"), and the publisher of the Joho newspaper is a counterpart to J. Jonah Jameson.

Note: 7 out of the 13 Japanese stories in total were fully translated by Marvel, with heavy edits to remove the violent scenes. After that the title was cancelled, which was a likely decision by Marvel since the stories written by Hirai departed even further from the source material, and included scenes of sexual and gruesome imagery of a kind not seen in the original US comic.

Our world is too normal. Heroic fantasy is much better, isn't it? Follow the adventures of an apprentice magician, her talking cat, and two great heroes... NOTE: French OEL

The main character Haruto who has the marking of a supreme king, unknowingly opened and entered the gate to the world of divine spirits. There he meets Feilen-kamisama who makes a contract with Haruto for an unexpected reason. Later Raika, nation of thunder, comes along and makes things more confusing for Haruto! What happens after this? A riot that flips his life upside down… or flat to the ground… NOTE: On hiatus

Teacher Hisoka wakes up to find that he has died and is now inhabiting the body of the student he tried to save. This is due to the interference of a monk, who informs him that he cannot tell anyone who he really is or the bond between him and his "new" body will break and he will die for real. Hisoka chooses to retain his memories despite the monk's warning that it will cause trouble....No doubt it will, since Hisoka is the type who cannot pass someone in trouble without trying to help!

What is love? A middle-school boy suddenly finds himself confronted with this momentous question.

The story of Kameda-kun's first love, told by his friend.

Teishu Academy is a school for the wealthy, high classed students that the upperclassmen can offer. Being at such high class the Socie, a school group that is almost like security, keeps a lookout for anyone who tries to bring in any portion of lower class culture. An example of this is an anime based keychain, which is a Rank 1 unacceptable item on campus ground. Those who break the rules are then crucified and called "Criminaes" and are set to be shamed by the public. Due to an increase in the number of such Criminaes, Hajime, the Shvarie du la Fleur of the Socie, has announced that the Socie will conduct unscheduled searches through each student's bag. A new student, Rentarou, is shocked at this since he accidentally had anime related material hidden inside his bag. He desperately tries to run from the Socie, but gets caught by the Socie leader herself! But instead of a severe punishment, the Socie leader, Ayako, decides to have Rentarou join her in creating a doujin game.

Spinoff series of Kanojo ga Flag wo Oraretara

Prologue of "Cloud Atlas", a movie released in 2012, drawn by SIU, creator of "Tower of God".