From MangaHelpers:
Yasaka Tokiwa lives in an unusual time, and according to his dreams, it's about to become even stranger. He's been having a dream of a woman called Ri'in ever since the robot, who he calls Makina, came to his home. He and Makina attend the same school, where their other classmates include a secret ninja (Kusanagi Kanata) and a sorcerer (Yata Haruka).
When Tokiwa, the robot, the ninja, and the sorcerer rush to rescue the student council president from a demon, the boys find that they've all been having the same dream! What is going to happen to their world?

At a boarding girls' high school where every student is an assassin, they target only one life: "The Hare", who appears to be a girl named Ichinose Hare. Similarly, "Azuma Tokaku" is an assassin who transferred schools to target her, however she gradually became attracted to "Hare" and decided to protect her.

Extreme school life START!

From Kodansha:

Class troublemaker Ryu Yamada is already having a bad day when he stumbles down a staircase along with star student Urara Shiraishi. When he wakes up, he realizes they have switched bodies—and that Ryu has the power to trade places with anyone just by kissing them! After figuring out the workings behind this new and amazing ability, Ryu and Urara take full advantage of the situation to improve their lives. But with such an oddly amazing power, just how long will Ryu and Urara be able to keep their secret under wraps?

Yuki Anno just turned into a high school student, she's very nervous and what's worse, she is in a different class from her best friend Jiu. But she resolves to make new friends. Upon meeting Jiu's cousin, Yuki, who has the same name as her, will she be able to open up and show people who she really is?

From Yaoi Is Life:

Saichi and Kotetsu are drawing manga as a team while living in extreme poverty. At loss for an idea, both of them decided to write a “real BL” based on themselves! They rise to be a star in the BL world, but…?!

"The other short stories within explore a schoolboy crush that turns into something more, an antagonistic relationship between a wealthy heir and his crush, and the love life of Usaki, the editor of Saichi and Kotetsu’s stories" (June).

Mizuki gets confessed to by a boy in front of a special Mirror. Legend has it, that if you confess to someone you like in front of that mirror your wish comes true.
There is a slight Problem in this Equation: Mizuki is just a very feminine looking boy.
Also it seems that he caught the Attention of the Norse Trickster God Loki while glancing into the Mirror. Loki decides out of boredom to mess with Mizuki and turns him into a real Girl.

From MangaHelpers:

Shou lives out in the country. He has a big crush on his childhood friend Sora, but is afraid that she thinks of him only as a little brother. One day, Sora announces that she was abducted by aliens. Later that day, Shou confesses his feelings for her and she dies shortly afterward. Shou is still in shock from her loss, when an alien girl named Lila comes down from the sky. She has a disk that contains a brain scan of Sora, and she can run Sora's personality in her own body. She also wants to have a child with him. Will Shou be able to cope with all of these sudden changes, and will he be able to keep Sora with him after all?

Meguro Mito has always been made fun of for her chubby appearance. Her sole happiness is discussing her favorite role-play game with her two best friends. One day, while she is being bullied, a handsome classmate saves her. Is this the beginning of her first love?

A story about a long-necked girl's love life:
Kanoi Natsuki and her childhood friend Itsuki visit the same school and there seems to be more between them besides friendship. As a Rokurokubi, her quirk of stretching her neck is normal for her and her surroundings, but it's not always her choice to stretch it and although she has feelings for Itsuki, she can't tell him what she feels. Ultimately, she has to go through misunderstandings and shame.
Itsuki, meanwhile, manages to make any awkward situations dissolve or maybe not?

From Shoujo Crusade:

What does it mean to be in love? Inoue Fuuko has a huge crush on the handsome Takamiya-senpai but due to her over the top delusions, she's mistaken as a stalker. Even though Fuuko really likes her senpai, she just doesn't know how to approach him without her delusions being triggered! Find out what this total amateur in love will do to get her beloved's attention!

From Black Lilac Scans:

What's it like to have a personal cook with great culinary skills and dashing looks? Sumika, an orphan, has one such personal cook, Miyoshi, who takes care of her needs. Miyoshi never complains but caries out his duties to the very end. But is it all just an act of duty? Does Sumika really understand how Miyoshi feels or does she take Miyoshi for granted? Follow Miyoshi and Sumika through trails and tribulations and witness a beautiful love story blossom~!

From Serenus Dreamers:
Aoi - a girl who lives in a household of seven. Her current status? Poor. Masafumi, dubbed the Prince of School, lives in a mansion with a household of mostly servants and his grandparents. His current status? Rich. When Masafumi decides to throw away 40 cents which Aoi could have used, she's enraged at his action of discarding the valuable amount, and vows to never forgive him! But, what happens when fate brings Aoi to the Prince's door, in place of her mother, who is injured? Revenge? Schooling in the antics of the poor?

Extra:
That is Why we Dream - Nakahara has a habit of setting things on fire, she coops herself up in the art room and never smiles..she is also a young and famous artist. While setting fire to another object, she meets a boy, who is a young and famous basketball player...why does he give her so much attention when everyone else shuns her? and why does she seem so sad while painting?

Misaki Hayato returns to his hometown and enrolls in the same high school as his two childhood friends. A lot has changed in the years he has been gone, his former best friends are seemingly distant from each other and leading relatively normal high school lives. Hayato's sudden arrival soon changes that and sends shockwaves through the entire town's delinquent population with his willingness to do anything for his friends and his love for a good fight.

Tsunagu's a high-school girl who admires the famous, beautiful and distant imperial prince: Takahito Ninomiya. Tsunagu's life takes a new light with a new classmate, Haruhito, who amazingly - and suspiciously - looks exactly like the famous prince...

Short story about a girl with a monster face

"Three years ago, he had the same posture.
Three years ago, he had stood behind Miyuki.
Yes.... Compared to three years ago, it had changed."

Set three years prior to the present time, Tsuioku Hen tells the events that would change Miyuki's world drastically, as well as the events that led Tatsuya to become what he is now.

(Adaption of Light Novel v08)

A girl who can see the future. Another girl who knows if what you're telling is true or not.

After a mission gone awry, the doubtful main character, Rood, is sent to a famous magic school, Helios. Here, he must protect an important person's son who has a very bad time at the school.

From Lucia Rose:
Amane Mikiko, better known as Mikki, is an elementary school student who moves a lot and has to transfer schools often. As soon as she makes friends, she has to painfully say goodbye to them. She is determined to not make any new friends at her new school, but it doesn't exactly go her way. Especially when she meets a boy with the head of a cat! But hold on, he only looks like that in her eyes?