“The first person to cause me sorrow was of my own gender.” Tsubaki gets hurt by his classmate Kaoru, and Koutarou by his kind older brother. Yet, in their hearts, they still hold longing and deep devotion. Passion, heartache, despair, sadness… Loving with body and soul, this is the real life story of these boys.
(Source: Jmanga)

Ichihashi Nanao is an incredibly bright girl and the first to ever transfer into Mehabia Catholic School. The one God here, though, is the "Judicature Club," a school-sanctioned means of resolving student disputes. Its president and judge is the first person Nanao meets--Hanegi Raika, a handsome boy who looks like a girl. This highly selective club wants Nanao as a member, but while she may be unwilling to judge others, she may have no choice when she herself is judged.
Source: ShoujoMagic

Three childhood friends (men) were lamenting about their unhappy lives when a strange beauty with the power to stop time appeared. She introduced herself as an agent of an organization called "Society", and invited them to join a game: after 300 days, the most unhappy one would have all his wishes fulfilled. Who was this girl, and what would become of these three men?...

A low-price, high-quality apartment in the metropolitan area of Tokyo is nothing short of a miracle! It exists, but there's a catch -- tenants must be good-looking and pass an interview by the landlord!? This is a love comedy about what happens when beautiful people are all gathered under one roof!
credit: Shoujomagic.net

The young tenor singer Dimitri miraculously escaped with his life after a severe accident. But soon after that, strange cases of group-suicides started to happen all around him… A vampire-romanesque tale of love and survival!

1) Futari no Tame ni Sekai wa Aru no (2 chapters and an extra) Asukagawa Chiharu is student body president of Ushitora High. Kisaragi Kyou is student body president of Ushitora's rival school, Bishin Academy. That naturally makes Chiharu and Kyou bitter rivals as well, but the relationship they hesitate to flaunt in front of the public eye is one of... lovers! They even have sex at hotels and are an average (!?) couple!!

See "Soko wa Nemuri no Mori," story 02 : "The Star Knows Everything", for a side story of this manga.

2) Valentine Cinema

3) The Queen's Favorite

From ShoujoMagic:

Story 1: Automatic Angel
Serika, a high-school student, is known for being a well rounded girl with an attractive face and figure. She is clear-headed and has a talent for sports. But she's an... android!?

Vol. 2, Story 2: The Winter Was Trying to End
Tale of a high school professor and student.

Souta, who’s attending a confectionery school, is in a relationship with Saeko, a girl one year older than him. He fell in love at first sight with her four years ago, and right before Christmas last year, they finally had their first kiss. Because his girlfriend loves big chocolate, every day, Souta tries to polish his chocolate-making skill. Even when his girlfriend smells like cigarettes although she doesn’t smoke, even when she turns down his invitation to a date on Valentine’s day, he’s still not broken-hearted at all, and he still continues to love her…
(Source: Aerandria)

Sakurai Ichiko is a 29-year-old woman whose head contains council members (each with differing personalities) that dictate her every thought and decision. While waiting at the train station one day, she encounters Saotome, a man whom she met and made short conversation with at a drinking party with friends. Although she’s interested in him, being a much a older woman, Ichiko hesitates over whether or not she should approach him, causing a wave of uproar between her intracranial council members.
(Source: Asian Girls on Mopeds)

From Tokyopop:
It's senior year, and Rica is seriously stressed out. She's got more homework, exams, and papers than she can handle, and was recently dumped by her boyfriend. In other words: Life sucks! One day, she's chatting online when she meets three classmates who hate school as much as she does. Together, they hatch a plan to blow up the school when no one is present. The countdown is on for X-Day ...

Featured in this manga is a side story called The Last Supper.

From Miista MangaFox:

"Sensei, is this a boy or a girl?"
"Do you want to know?"

Ichijo Mashiro and fellow classmates are enlisted in a mysterious weekly class that takes the form of a shared nightmare. Like most teenagers, Mashiro has a secret.. he's neither fully male nor female!

So far, Mashiro's been able to live life as a boy, but all this changes when he's informed of a new class he 'must' partake in order to graduate from his elite preparatory school. To pass, he must find the key and the one way to find it is to enter into a nightmare world, where his body and soul are put at the mercy of the worst kind of enemies -- other school students, who are battling to find the key.

From renowned author Mizushiro Setona, comes a riveting epic mystery that lies between the students, that will have you engrossed from one page to the next. Happiness, sadness, blood and tears will all be shown, but which one leads to an ending? Take the next step into the world of After School Nightmare!

1) Twins:
Moe-rin (Moeka) attends an all girls school. Shino-chan (Shinobu) attends an all boys school. They're brother and sister twins who are very close, but Tori-chan (Professor Torikai) from the all boys school falls for Moe-rin at first sight, and Shino-chan is hot for Professor Mifuyu of the all girls school. They're still only just kids, but which twin will be first to have a sexual experience...?

2) Please Don't Stop Us [Watashi-tachi wo Tomenaide] :
A girl tries to create one final, ultimate memory for her boyfriend, who has to leave the country because of his father's work.

3) Central Kyoto Love Story [Shijou Riverside Town Love Story] :
The story of a girl who transfers to a Kyoto school and her experience with a temple master's son.

From ShoujoMagic:
A collection of short shounen-ai stories by Mizushiro Setona, all connected by the theme of plantlife.
[STORY 01] (English Title) Breakfast (Japanese Title) ブレックファスト (Romaji Title) Burekkufasuto: The tale of a boy who displays the symptoms of man-eating syndrome.
[STORY 02] (English Title) The Tale of the Ring (Japanese Title) 指輪物語 (Romaji Title) Yubiwa Monogatari: The tale of two boys who are dating each other and mutually hiding the fact that both are dating their teacher, who frets because a ring has been lost.
[STORY 03] (Japanese Title) Honey β: The tale of a flower that blooms by inhaling memories. But even if our memories are taken from us, some precious things are never forgotten. "I don't fear losing my memory if I can feel this way again tomorrow..."
[STORY 04] (English Title) Undying Illness (Japanese Title) フジノヤマイ (Romaji Title) Fuji no Yamai See "Mister Mermaid," story 2.
[STORY 05] (English Title) Aconite (Japanese Title) トリカブト (Romaji Title) Torikabuto

Shouko is still a virgin, and hasn't met a man yet who lives up to her standards. Her friends look up to her -- and would in truth like to give her more than just their respect -- but the only one Shouko looks up to is her famous actress mother, for whom no man is good enough to dedicate herself to. That's when Shouko meets the rumor and reality of her mother's new boyfriend, Ujou. Ujou is different from the others -- an aloof college student 17 years younger than Shouko's mother. The passion that Shouko sees between them becomes what Shouko desires for herself, but while forbidden fruit may be sweeter... it is also more deadly.
Vol. 2, Story 2: Angel Night
Right before we die, an angel comes to our side and waits for the moment when it can ferry our soul to Heaven. In the case of Rin, a pop singer who has just been dumped by her producer boyfriend, it's because her angel is present that she can't commit suicide. She can see the handsome angel Faye, who won't leave her side until his mission to collect her soul is complete...

Consists of three oneshots:

1) Soko wa Nemuri no Mori -
Yui has stopped growing because of something that happened when she was 12 years old. One day, 18-year-old Yuri found a young man with amnesia near the hidden cottage she lives in, and brought him home. Yui named the man "Pochi" because he cannot even remember his name, and she treats him as her pet...!! This is another story from Setona World that will shake your heart and soul!!

2) The Stars Knows Everything -
Futari no Tame ni Sekai wa Aru no extra.

3) Climb the Stairs of Cinderella.

A girl forces herself not to feel anymore after years of sexual abuse from the master of the house where her father is a chauffeur. But then her father and the master die in a car accident, and she's left to live with the two sons...who both want her.

Kyouichi is now divorced from his wife and carrying on a tenuous, homosexual relationship with Imagase. He has even become accustomed to having sex with Imagase every day. However, when Tamaki, a young co-worker with a crush on Kyouichi, appears on the scene, it might be the beginning of the end for Kyouichi and Imagase.
(Source: presencedear)