From Seven Seas:

Being a girl is harder than it looks...
For Hazumu, this couldn't be more true, because just the other day, she...was a he.

Shunned by the girl of his dreams, Hazumu loses himself in the mountains and is promptly squashed by an oncoming space ship. The alien inside, feeling guilty, rebuilds Hazumu's body...but as the wrong gender!

Now Hazumu must learn how to be the girl his parents always wanted while dealing with the trials and tribulations of being caught in a love triangle between two girls--his childhood friend, Tomari, and Yasuna, the girl who rejected him but is now strangely attracted to him/her!

This is a 4-koma featuring the high-school kid Kei, and his childhood friend Rin, who loves paper airplanes. Kei seems to like Rin, though he's somewhat oblivious to his own feelings. With the addition of Rin's classmate Ryuusuke, who shares her love of paper airplanes, and another new character, Aoi, Kei's emotions become more and more complicated. Apparently feelings, like paper airplanes, don't fly straight.

King Panda is dead and the Upper Yard of the Zoo is left without a ruler. The animals of the East jockey for domination while the peaceful animals of the West prepare for the oncoming war. It's the cutest and funniest animal civil war you'll ever see!

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 Broccoli:

Ren just wants to be one of the cool kids, but it doesn’t help that secretly he’s just a nerdy monster fanatic. That is, until a young girl named Kokon shows up. She claims to be a fox that he had helped years ago and now she wants to return the favor.

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.

Maeda Hachibei is unlike most guys, who lust after gorgeous girls. This pervert lusts after their discrete parts, instead. When he moves to Tokyo to attend school, he finds himself living in a dormitory with five girls, each of which possesses one of the ideal physical features he desires: gorgeous blue eyes, bullet-train breasts, a deep dulcet voice, straight “anime-esque” legs, or a waistline shaped like fine Japanese pottery. How can he manage to keep his wits when surrounded by these women? If you think this sounds like a Love Hina clone, you wouldn’t be entirely incorrect… but Hachibei isn’t Keitaro.

Includes a oneshot in Vol.12: "The Boy Who Heard Too Much".

Touma Outa wakes up from a bad dream one morning and when he sees his reflection, there are horns growing out of his head. Suddenly, he is pounded in the head by a cute, hammer-carrying knight from the demon world. The horns shrink, but he is not off the hook yet, for the little knight, Pukateriosu, is there to prevent him from transforming completely into the Demon King whose soul has entered Outa's body. The PukaPuka hammer can return him to normal but it takes time to charge. In the meanwhile, Outa must try not to think worldly thoughts or be kissed, but it's easier said than done with his crush Shirayuki Himeka, the little demon Garbelion, and even Pukateriosu around...

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.