From Angelic Powder:
The princess of love, Koiko is given the power to zap people to admire her but the power will leave her when she reaches adulthood and marries. There was one boy she had never zapped before, Shirou. But he turns out to be someone different when he doesn't show up as he promised. Koiko being heartbroken runs to find him, only to find new things she never knew about him. It turns out he is one of the legendary shadow ninjas.

From Hochuuami:

A bored magician, Kei, meets Takanashi who is supposedly a card dealer on the cruise ship he's working on. He truly has no idea what's in store for him when he runs across Takanashi. For starters, how about a game of... strip poker?

A manga about pirates, from Yuri Hime's cell phone line. A young woman infiltrates a band of pirates to try and get back a treasure that they stole from her mother.

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.

Sherbet Lemon and Covenant of Darkness:

The snow mountain is his territory, no one is suppose to live there! Who is this daredevil?! How dare he chop off my favorite gingko tree. To make it worse, he took all the furnitures in my cave! Darn! I won't be a demon fox if I didn't take revenge! But... he's just an idiotic scholar, why can't I get close to him? When the mischievous but innocent snow fox meets a slow yet scheming scholar, the truth isn't what Xue Qiu expected.

From Aerandria Scans:
In this grim and realistic take on classic fairy tales, Prince Ludwig, a female corpse collector, is ordered by his father to find himself a wife more suitable than the women he often brings into the castle. Along with his servant Wilhelm, they travel across the land in search of fair maidens from classic stories in hopes of finding Ludwig a wife.

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!

In a world where demons and humans are at war, there exists a Demon King, whose voice holds a power that destroys all in its way. When an unusual Hero attacks his castle, what's a Demon King to do other than confess his love? But thanks to meddling minions and the inconvenience of a voice that destroys everything in its path, his confession may not go according to plan...

Tezuka teaches about biology in short installments.

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}

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.

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.

From the exciting new animated chapter of Ash and Pikachu! Shaymin, the peaceful Gratitude Pokémon, lives happily in forests and fields of flowers. But one day Shaymin is accidentally drawn into a battle between the Legendary Pokémon Giratina and Dialga. Whisked away far from home, Shaymin is found by Ash, Dawn and Brock, who soon discover that this new Pokémon is full of surprises! Of course Team Rocket wants to get their hands on Shaymin, and so does a mysterious man named Zero. Even Giratina is in hot pursuit of this little Pokémon—and just what do Giratina and Shaymin have to do with the dimension known as the Reverse World?

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.

From TokyoPop:

After 1000 years of peace, the wolf god Fenris Fenrir has been reborn. She seeks to find the reincarnation of Balder, the most beloved God, as the land of Midgard sinks further into anarchy. They are both key players in the coming of Ragnarok, the time when fate and free-will shall come into conflict as the very nature of the universe is forever redefined.

RilleL:
Based on norse mythology, ragnarök is the term for the end of the world. Christian equivalence would be the last judgement.

The popular Korean MMORPG "Ragnarok Online" was based on this book.

From Tokyopop:
On a world with no women, the surviving men have reintroduced the female in the form of an android. Called Marionettes, they are built to serve men and are limited in their interactions with humans. That is until a poor boy named Otaru Mamiya encounters a Marionette named Lime. Lime is a Saber model with a special circuit that gives her emotions. When Otaru awakens two more Saber Marionettes, his life as an 'average' man quickly becomes as extraordinary as the lives of his eager, busty new friends.