From Chibi Manga:

Because she loved drawing and wanted to do something special, she went to a famous art school.
And there she met the handsome and cool guy...

From Divine Sanctuary:
Ever since she was small, Sakurako has always been treated nicely by all the boys she meets. That made her get too full of herself, and one day, she caused a boy to be hurt very badly. If only she can meet him again to apologize and tell him her true feelings...

Plot revolves around high school freshman Shingo Susa as he is invited by his crush from middle school Sayuri Shiroyuki to the school's supernatural club. Over the course of the series Susa begins to gain supernatural powers, something that prodigy Rei Uryu, attempts to awaken to bring out the psychic giant, Susano Oh to destroy humanity and establish a new world order.

Won the 4th Kodansha Manga Award for Shounen in 1980.

From MangaHelpers:

Takahashi Ena is a high-school idol with a secret hobby. She often wears headphones, and people assume she is listening to music. In actuality, there is no music playing; she is eavesdropping! She prefers to listen to two of her male classmates, Nara and Mikage, because they have the most interesting conversations. She has to be careful to not be found out, though, because a creepy hobby like that could ruin her image! [tethysdust]

From Midnight Scans:

Kureha Mimachi, a 15-year-old girl, has just transferred into Shiritsu Kenhono High School. However, there is something weird about this school, it is actually a school where the Princes and Princesses of the beast-kind go to!

Even though Kureha is human, she is there as a way to help the students lead their lives peacefully with humans and has the role as the "rabbit". Will she be able survive without being eaten by the students? Only time and her hidden bodyguards will be able to answer that...

The Freezing Pair Love Stories manga tells the story of how the various Pandoras and Limiters met. The first chapter focuses on the characters Ganessa Roland and Arthur Crypton.

Since the beginning of time ninjas have been regarded as people with great skill and power, the Blazing NinjaMan (Shinobi Mantaro) is one such young man. There is only one problem, the era of the ninja has come and gone. How can Shinobi consider himself a ninja in modern day Japan (1990s) and survive the daily rigors of high school life.

I love math. Just after the high-school entrance ceremony, I meet a beautiful girl: Milka. Milka is a mathematical genius. She shows me many math and many elegant solutions. Milka and I spend a long time discussing math in the school library.

One year later, I meet another mathematical girl: Tetra. Tetra is one year younger than me, and asks me to teach her math. While I teach her, she begins to understand math and gradually to love its elegance.

The third series is about logic puzzles, Peano arithmetic, epsilon-delta, Cantor's diagonal argument, Hilbert's program and Gödel's Incompleteness Theorems.

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~!