Rinne Ikaruga is just your average 16 year old girl, trying her best to get by. One day, she receives a package addressed from her sister, inside of which is a little girl who just happens to be part planarian and can multiply.
A planarian is a kind of non-parasitic flatworm organism.

Pilot for D. Gray-Man.(http://mangapark.com/search?q=dgray-man)

Fujita is a second year middle school student with a face as pretty as a girl's. On top of that he's whimpy and a bit of a crybaby so he's often confused for a girl. Echo-chan is a fairy who promises to grant his wish and turn him into a strong and attractive man capable of sweeping Onigasaki, his unrequited love, off her feet if he agrees to help her.

From Karma Falls Scanslations:

Because of a frightening experience three years ago, the boy Sata Senda became a compulsive cleanliness freak. As he has anti-bacterial spray and mask as standard equipment and doesn’t allow any form of close contact, he has no friends… Thus came the summer of sixth grade. Sata, who has been half forced to participate in the school trip, arrives to the meeting place completely wrapped in a protective suit?!

From Transcendence:
High school student Asahi is forced to provide blood to a childlike vampire Hikato, and becomes his "temporary" mother, until he reverts to his original self. When Asahi finds out that Hikato stayed behind to protect the human world, how will her thoughts towards him change….!?

From Taruby:

Our protagonist, Moji Shimeta, just so happens to fulfill the stereotype for being a worthless human. His inability to carry out a conversation has left him at the bottom of the barrel as far as friends are concerned.
That Shimeta fell in love with the school idol Ishikawa Yuuko, however that kind of love is absolutely, perfectly, and completely impossible. During this time, the messenger of the gods, Osaki, appeared to grant Moji's request with a price attached concerning Moji's cooperation in catching some runaway evil spirits. However to catch them all, Osaki uses Moji as a vessel to become a servent of Uganomitamanokami (aka Inari) called Youko. Lots of Ecchi situations and humiliation abound at Moji's expense.

Ohisama Egao collects the stories of the budding romances of three schoolgirls and one teacher - Aoi, Ryouko, Shizu, and Awada-Sensei - and also shows how their lives intersect at school, a small cafe, and elsewhere. Things don't always go smoothly with the schoolboys they like, but like the sunflowers that surround them, the girls keep looking for the sun.

- polm23

In the Noramimi universe, most families own a 'mascot'. These strange and amusing creatures live at home and act as companions for younger children.

Noramimi is one such mascot. Unfortunately for him, he is an ogre type and thus not popular with children, who prefer 'cuter' alternatives. Unwillingly, he decides to 'home stay' at "Hello Kids" - an agency that organizes matters between mascots and humans.

But, like all mascots, his heartfelt wish is to one day be adopted by a family...

The son of a famous pianist, music student Shinichi Chiaki dreams of studying abroad and becoming a conductor like his mentor. Unfortunately, his fear of flying grounds his lofty plans! As he watches other classmates achieve what he has always wanted, Shinichi wonders if he should quit music altogether.
Then one day he meets fellow student Megumi Noda, also known as Nodame. This oddball girl cannot cook, clean, or even read a music score, but she can play the piano in incomparable Cantabile style. And she teaches Chiaki something that he has forgotten: to enjoy his music, no matter where he is.

Winner of the Kodansha Manga Award for Shoujo in 2004.

This is a story about 2 childhood friends, Masato and Yuki, that reunite as teenagers. Masato is surprised to find that Yuki has become so cute, but even more surprised to realize that Yuki was, and still is, a guy. Yuki's affection for cross-dressing leaves Masato with feelings of discomfort and fright.

On the last day of school, Mihane confesses to her senpai the long-term admiration she's had for her ever since they met, as well as tells her that she will try her best to enter Niji no Oka Girls' Academy next year, the school to which her Senpai is going to attend. Now, one year later, she's managed to pass the entrance exam to the prestigious school and is taking the bus to the school. Unfortunately, she takes the wrong bus, but encounters an interesting first-year girl, like her, that is also set to attend Niji no Oka Academy.

Hilarious!

The Hinomoto Kingdom's Princess Guard is an elite squad that directly protects their royal princess. Kasuga Haru was newly appointed to this prestigious position and was stationed next to the Kingdom's one and only princess.

There's only one problem. Their "royal princess" is a hikikomori, a recluse who stuffs her room with video games and refuses to leave even a nanometer-length out of her room, much less let anyone in. Kasuga's special mission given by the Queen is to make Princess Terras into a proper human. Can Kasuga succeed in turning this otaku princess into a proper princess full of charm and beauty?

Yoshino Nako has a saying. "If I'm happy, I can do anything!"

In her sister's place, Nako-chan steals the groom of an arranged (political) marriage and helps them elope. But when the Hayami group starts failing, she must pay the consequence by housing the delinquent brother...

From Perfect Illusions:

Reo-chan, a first-year girl, gets dumped by her boyfriend because she's not skilled in the home economic traits he believes women should have. Her ex tells her that she must apply to a "housework" club before he will reconsider going out with her. Therefore Reo-chan has little choice but to join.

Here's the catch: the only members are four gorgeous bishies. The other first year in the club, Irinaka, competes with her a lot. As the story progresses Reo and Irinaka get forced into a lot of interesting situations together and in the meantime become closer and closer.

Being beautiful is never easy, especially if you're an eighteen year old boy like Yoon Da In who is constantly mistaken for a girl because of his delicate good looks. Da In is, in fact, anything but delicate. He is the ringleader of a group of tough kids in an all boy's school, and he's quick to beat the living daylights out of anyone who even hints that he resembles a girl. If that wasn't hard enough for a regular teenage guy to cope with, his life is about to take a shocking turn for the worse. When Da In stumbles upon strange happenings in the forest, he gets sucked into a world of vampire intrigue and sinister romance that he never knew existed. And he learns that there are worse things than being turned into a vampire: being turned into a girl?!

Momoko is a girl who was born into a witch family in which most of its female members possess magics. Yet they can only reveal their magical capability to "the one" i.e. their soul mate/spouse. The more magic she uses in front of strangers, the more parts of her body would become cat-ish (such as cat ears and whiskers), and if any stranger learns her true identity she would turn into a cat completely--like her mother!

Having joined the magic club in her school, Momoko has used her ability too often that her cat ears pop out every once in a while so she must find "the one" as soon as possible, but her candidates have already become suspicious...

Confident and in beautiful personalities develop projects for the Spartan models begins!

Matsuri Ichimatsu, Haruno Koume, and Sanguubashi Takezou are old friends with one thing in common: despite their good looks, they're incredibly unpopular with the ladies. But what does Polaris have to do with their fate? And will they ever get that harem they've always wanted?

It's the start of high school, and Kako decides to "produce" her bookworm of a childhood friend, Kousei, so that he can become a good-looking and popular school idol. She models him after Lawrence, a character in a manga she likes, but as Kousei's transformation becomes a huge success and he extends his new character beyond what she asks for, what will Kako do? Will she find herself left behind in the wake of his newly found popularity?

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Also included is a story called Megane Danshi Shinka Setsu (Theory of Evolution for guys with Glasses) in volume four.

Twenty-nine-year old Kurose Kazumi is a programmer in an eroge company and has played plenty of galges when he was younger, but he's completely uninterested in young girls. A chance encounter changes that when a confused middle schooler approaches him due to a misunderstanding, but he realizes how sweet she is and wants to keep meeting her.