Rain Jewlitt, known as the Methuselah, is a spaced-out, immortal, 624-year-old man dressed in priest's clothes. He's got eternal youth and a large price on his head—put there by those questing after the secret of his immortality.

Machika Balfaltin is a tomboyish, energetic 14-year-old girl who, upon the death of her grandfather, sets out to kill Methuselah, the one bounty her assassin grandfather, Zol the Grim Reaper, couldn't kill. Instead, however, Machika ends up being saved by Rain again and again from other aspiring bounty hunters attacking them both.

Sound like the beginnings of an odd relationship? You won't believe where their journey takes them...

Japanese yakuza clan heir Ranmaru just got married on a lavish cruise ship, but things aren't as they seem. The marriage is just for the appearances, and he ends up getting drunk and spending the night not with his bride but with the sexy ship captain. When the two men meet again in Italy, it is the start of a spectacular love story.

Includes an extra story called Koi no Annainin (The Guide of Love).

Tsuna comes home one day, only to be greeted by a little baby mafioso who apparently is his new home tutor. His job is to guide Tsuna into his role as the 10th Boss of the Vongola mafia family. With the help of all his new friends and an array of special items such as the "Dying Will Bullet", he might just be able to do it.

From Yen Press

Soon after his birth as a Nobody, Roxas joins the mysterious Organization XIII, knowing nothing of his identity. With the help of Axel, another member of the Organization, and the mysterious No. 14, who is also missing her memories, Roxas slowly begins to learn what it takes to be a part of Organization XIII…and what it means to have a heart.

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.