From Endless Abyss:

The Law of Ueki plus takes place 2 years after the end of The Law of Ueki, everyone has gone there own way and life has become peaceful again until one day Ueki saves a dog only to stumble upon a plot to steal the memories from all the people of earth. Ueki as the only person who did not have his memories taken, must go into a new world and retrieve the stolen memories where new allies, foes and powers await.

A group of powerful beings called tenkaijin are holding a special tournament. The rules of the game--each tenkaijin selects a kid in junior high to be his champion and grants him a special power. The kids take each other on in heated battle, but if they hurt innocent bystanders, then they lose one of their natural-given abilities. Every time they win a battle, they gain a new ability. The ultimate winner of the tournament is granted any power of his choosing, and the tenkajin who he represents succeeds in becoming the next god. Kosuke Ueki has been chosen to fight in the tournament. His special power--the ability to turn garbage into trees.

A school mahjong story about the everyday life of middle schooler Asakura Yoshiaki, his classmates, teacher, underclassmen, and the other members of the mahjong club.

Based on DS Dating Sim "Love Plus"

This is a collection of short stories by Suihei Kiki that were serialised in the Seasonal Gangan Powered magazine's 2003 Winter issue all the way to its 2004 Winter issue. Ignoring the tame nature of Suihei Kiki's debut work "Mahou Shoujo Rukana", Suihei's "Mika ni Harassment" short stories are extremely ecchi in nature for a manga serialised in a shounen magazine aimed towards children. Ecchi to the point that the compilation in March 2005 was jokingly advertised as Square-Enix's first adult manga.

Mika ni Harassment: In the first story, Mika makes a wish on a mirror in order to change the world into one where boys don't have ecchi thoughts when they look at girls. In the second story, Mika's school falls under the control of a misogynic dog who hates high school girls (which includes Mika). Finally, in the third story, Mika raises the ire of six-year-old child genius, Kokoa, who forces Mika to attend kindergarten again.
Kasumi Otoko no Ko: A story about a girl called Kasumi who is a tomboy. One day, Kasumi's friend, Haruna, gives Kasumi a Chinese doll that supposedly houses an ancient Chinese goddess of femininity. Kasumi drops the doll into a ditch, which causes the doll to seek revenge on Kasumi.
Mahou Shoujo Rukana: A story about a boy named Shuuichi, who has a special power that lets him communicate with animals. One day, Shuuichi moves in with a scientist who wants to study Shuuichi's special abilities. Also, the scientist's daughter is a magical girl called Rukana. Though, Rukana breaks many magical girl stereotypes.

Note: The author published sequels in form of hentai Doujinshi.

The Norse god of mischief Loki has been banished to the human world in the body of a young boy. In order to redeem himself, he sets up a detective agency and dispels the evil residing in people's hearts. He is joined by Mayura, a spiritually clueless high school girl with a passion for mysteries, and eventually, other Norse gods begin appearing around Loki for unknown reasons.

From Project Bite Me! Scanlations:

The creator of Baoh and Jojo's Bizarre Adventure presents a manga about magic and mysteries! You'll meet him at 13:13 pm, on Friday the 13th. He'll do an uncanny intro where he plays a trick on you! And wherever he goes, trouble seems to always follow. Who is this person who creates such incidents? None other than Cool Shock BT!

From CPM:

An alien armada from Jupiter has amassed enough power to destroy all of Earth's defences. Earth's final hope lies in the Space Battleship Nadesico, a ship created using recently discovered extraterrestrial technology.
Can the Nadesico's rag-tag crew overcome their idiosyncrasies and defeat the alien fleet, or will Earth's last hope be lost?

The manga differs greatly from the anime

[From Viz]:

Ginta Toramizu is a 14-year-old kid who doesn't have a lot going for him: he's near-sighted, doesn't do well in school, sucks at sports, and to top it off--he's short! But Ginta is a dreamer and has had the same dream 102 times, always in the same fantasy world, where he is a hero blessed with all the abilities he lacks in real life.

Then one day a supernatural figure appears at Ginta's school and summons him to a mysterious and exciting new world! In this strange universe filled with magic and wonder, he is strong, tough, agile--and he can see without his glasses! Thus, Ginta begins a mystical quest in search of the magical items known as "ÄRMS," one of which may have the power to send him home. Joining him on this epic journey are his companion Jack and the valuable living, talking, mustachioed iron-ball weapon known as "Babbo," which everyone wants but, it seems, only Ginta can possess!

Clay, a child prodigy, was hired at the age of 14 to become a professor to make chimeras, creatures made with a fusion of various materials. However, after he was hired, he was unable to meet the expectations of the company that hired him and was fired. He comes upon an abandoned research facility and creates a human child chimera and names him Muddy. Together, they will go out into the world and find out what Muddy is capable of.

From Tokyopop: Nanaki survives a car accident to discover he is psychic. Recruited into an organization that solves cases with psychic powers, Nanaki's average life quickly turns into one of adventure and intrigue. Slacker Nanaki Shunsuke's life is turned upside down when he's hit by a bank robber's car and later meets a strange boy who claims that the accident caused Nanaki to develop psychic powers and that he is required to join LOCK, a paranormal investigations agency or be the suspect of any and every suspicious case that turns up. (thought a summary and categories were need since there weren't any :P If your into Shonen it's a good read :P Sirenic Griffin){Corrections by Silvermagic}

This manga takes place in a school where the students are based on famous shoguns in Japanese history. Sengoku Gakuen was once like a normal school but Oda Nobunaga, the student president overthrew the teachers and practically made them powerless. He built a school of the students, for the students and by the students. Nobunaga eventually graduated and left Hideyoshi in charge as the student president. However, Hideyoshi soon drops out of school to help Nobunaga rule Japan as he ruled Sengoku Gakuen. The story picks up here as there is a battle between Ishida Mitsunari, an uptight and conservative, yet hardworking boy, and Tokugawa Ieyasu, the temporary school president who has lots of followers, fighting for the school president seat. We also see other famous figures as fellow students such as Ootani Yoshitsugu who is loyally following Mitsunari and Oichi, Nobunaga�™s younger sister. Who will win the student body president position and take command of the school?

?Onegai Twins? is a cute, incestuous love story between a boy and two girls who are supposedly his long-lost twin sisters. The story follows Maiku, Karen, and Miina. Maiku is a high school boy orphaned at an early age, now living in a house he believes is the house he grew up in. Onegai Twins! is the sequel spin-off to Onegai Teacher!

From Broccoli:
When Kaya runs into trouble one day, it’s not a knight in shining armor, but her stuffed animals that come to her rescue. It may sound crazy, but Kaya isn’t pretending: she loves her stuffed animals so much, they come to life and turn into people! Plushies come in all different shapes and sizes, and so do their hearts—whereas some are nice, there are others who are not so kind.

Keisuke and Makura are childhood friends who grew up together almost like brother and sister. One day, due to a misunderstanding they had, Makura left the house angry until Keisuke's Mom is worried about Makura not coming home yet, thus Keisuke is told to go look for her. Reluctantly, Keisuke went out to find Makura, He ended up at a place they used to go often, the sunflower field. Luckily, Makura was there. Keisuke joined her sitting on the bench and they began to reminiscence. When Keisuke decided that they should head back home, he phoned her mom to say that he found Makura, only to be shocked when her mom told him in panic to head to the hospital. At that same moment, he looked at Makura, who was not standing but floating in the air...

Ash may think he's seen everything when it comes to Pokemon, but is he ready to face the mysterious Darkrai in his latest awesome adventure? While touring Alamos Town, home of the Space-Time Towers, Ash and his friends discover that the town's special garden has been ransacked. Some of the townspeople immediately blame the destruction on Darkrai, a sinister-looking Pokemon said to haunt the garden. But is Darkrai alone responsible for all the strange happenings around town? And what is its true nature? Will Ash and his friends discover the answers in time to save Alamos Town? There is a movie of this.

Rocket Princess was written by Nobuyuki Anzai before he started his work on Flame of Recca.

Basically, we follow Ishibashi Kango through his days as he interacts with a cyborg by the name of Oozora Kohime.

If you liked Flame of Recca, then I'm pretty sure you'll find something to like in this one, too.

The Continent of Song is in chaos. The sinister secret society known as Demon Card is using the power of Dark Bring to destroy everything in their path.

The only things capable of stopping Dark Bring are the Rave stones. Unfortunately, the Rave Stones were scattered around the globe in an explosion 50 years ago, so now they must be collected by the Rave Master in order to stop Dark Bring once and for all.

This new task has been given to Haru Glory, a sixteen year old boy from Garage Island.

The World's fate now rests on the new, young Rave Master.

Asaka, the prison's nurse, is leaving her post to her gorgeous granddaughter Yuki, who will bring a lot of troubles and chaos in the life of the people around her, starting with detective Tatsumi, her childhood friend and now her neighbor.