In the distant future, humanity is now only made up of women. Kohane Sumino has just enrolled into the prestigious Shirasakuya Academy that contains within it a secluded courtyard garden maintained by the Gardening Club. Legend has it that if two people pledge their love for each other underneath a pair of trees in that garden, they will be bound for eternity. Kohane seeks out the garden on her first day of school, where she meets Rekka Hanatsuka, the friendly self-proclaimed acting president of the Gardening Club. Although Kohane proves to be fairly popular early on, she soon learns that paradise is not without its thorns.

From DMP: Why is Toru Kouno receiving such an overly warm welcome at his new all boy's school? He has yet to discover the secret system called "Hime (Princess)" in effect at the school. Boys who are chosen have to dress up as a girl in every school event! Little does Kouno know that he would be the chosen one... -- Contains the story Tore x Puri (Train x Princess) in volume three.

A oneshot about two teens hiding who they are from the rest of society, one perceived as a genius and the other perceived as a delinquent, and how their true selves come together and change their perception of the trivial everyday.

Akira Shiraishi, a young high-school boy with feminine features, joins Blaue Rosen, the all-girl band that Mizuki Sakurazaka, an androgynous girl of the same age, performs lead electric guitar in.

Their high-school life is anything but typical: Mizuki is the "prince" of her all-girl school while Akira is the "princess" of the neighboring all-boy school. A series of comical events brings them closer together, even as the prejudice of the people around them tries to hold them back.

From Musume:

This manga revolves around a super-shy girl named Mugi Asai who gets forced into joining the Drama Research Society at her new high school.

Kohane, a high school student who has a bad pronunciation since she was young. She refuses to talk since she's been teased by others because of her accent and chooses rather not to, than being laughed at. One day, when Kohane was going to the teacher's lounge, she meets a senpai who had wounds from a fight and gives him bandages since there was no nurse in the office. Igarashi (the senior) confesses to Kohane and helps out for her English pronunciation contest. The story is about Kohane accepting herself and finding someone who accepts herself with her awkward accent.

Makabe Masamune has changed himself greatly for a single reason: he wants revenge. Contrary to his past, he has worked hard to become good-looking in order to carry out this goal. Faster than anticipated, he even meets the target of his revenge the first day after transferring in.. Adagaki Aki! He wastes no time beginning his plan, but revenge doesn't come easily.

To search for a missing friend, six people go to a closed theme park "Birdcage Castle" which they thought to be deserted.
However, in there, groups of two people are chained to each other and the game of death begins.

From MangaHelpers:
Ando Hanaka wanted to become stronger because she thought she couldn't protect her friend from bullies. Now as she enters high school, she seeks to enter many of the martial arts clubs in her school. Unfortunately for her, many of the clubs reject her due to her frail and small size. She just wants to be stronger, but is it going to be impossible for her?
All of this changes as she encounters her classmate Yoshino "Koha" Koharu. Koha introduces Hanaka to the world of MMA. Hanaka learns that martial arts is designed to make the weak stronger. Her aspirations of becoming stronger may come true as she ventures into the world of mixed martial arts.

This is early 1980 where there is no internet or cell phone. Jo Umeyoshi, who plays around, meets Chihiro Sakagami and falls in love with him. Umeyoshi is excited and thinks that Chihiro is his destiny. On the other hand, Chihiro, who has a famous father, couldn’t figure out why he had to exist. And Chihiro starts to have feelings for Jo who is a very unique and right kind of a guy?

In junior high, Aikou had a crush on his tutor that ended badly. Now in high school, he's joined a "kiss club" at a local bar to try and relearn about love starting with the basics. While holding up a "free kisses" sign in the park one day, he's spotted by Eisuke, a boy from his school. Intrigued by Aikou's sign, Eisuke impulsively kisses him. Could this kiss be Aikou's chance to start over?

Semimaru is a loner with his only redeeming feature to be studying. Visiting him every night is his female childhood friend, Mika. During an accident, she became a gluttonous spirit ghost while in coma and said, "I cant die because my stomach is empty!". Since then, to let Mika die in peace, he cooks meals and dishes for Mika. However, eventually, the meals slowly change into a "For Mika to Live" cuisine of handmade dishes to preserve her spirit. This is heartwarming story.

From Tokyopop: Before Ekichi Onizuka would become "Great Teacher Onizuka". He and Ryuji Danma were the leaders of the famous biker gang, Oni Baku. When they weren't out riding around and getting into trouble, this duo could be found in school. Doing what you ask? Picking up young women of course!

You may also like:
+ Inu Yashiki
+ Kingdom

It happened in a sunny day right before summer. Fujisawa Souta's first kiss was with his older classmate, Ayase Chihiro. It's now their summer vacation, and yet, nothing has happened between the two of them! What's worse? he discovers that he wasn't actually Ayase's first kiss, and now regrets kissing him.

story 1: Akari is in the library committee and dreams of a love life like those in romance novels. Akari wants her first kiss to be like those in the novels, but when a player at school suddenly kisses her... what will become of her love life? story 2: Takano Kaya have been skating for the past 7 years but she still lacks the proper technic, but a guy shows up and draws a picture of her soaring with wings. Can she really reach her dreams?

10 years ago a child wished for the destruction of the world. Now a Group of people has the ability which grants their wishes depending on their power.
They are called "Order User". Before these great people who has the power of "Order", one person excels most, with the ability to rule and conquer the world and turn people into puppets when it is on his Jurisdiction. That power belongs to Hoshimiya Eiji, who is also responsible with the destructive phenomena happened exactly 10 years ago.

Mei Ishizawa is a really shy girl that gets extremely nervous around popular people, particularly her desk neighbor Sasahara-kun, where she trembles at his presence. Can Mei face her fears and get close to Sasahara-kun?

From YaoiSM 801:

Kiyonaga Akane, a new delinquent who’s weak at fighting but has a strong will. One day, he got beaten up by Yankees from another school, then, his hero - Kidou Ryouji and Kurokawa Tarou saved him. They became closer and Kurokawa keep teasing Akane every day. Not only that, Kurokawa also do perverted things with Akane?!

Tsubasa is studying at music high school. somewhere in the darkness, meeting with him, changes her destiny?