From Yaoi Is Life:

In Spring of his junior high 2nd year, Saitou got in the same class as Suzuki. Receiving Saitou's help while being bullied in first year, Suzuki smiled shyly while thinking, "what if we became friends". Saitou is becoming more and more conscious about Suzuki and their relationship starts to change?!

Including the continuation of Bokura ni Matsuwaru, etc. (You & Me, etc.), Bokura no Ashita no Houteishiki (The Equation to Our Future), and Sono Te Kara Tsutawaru (I Can Tell by Your Hand).

From Nakama:

Koudou and Takashi are lovers. But there’s one cause of uneasiness. Koudou is just a popular guy. One day, that uneasiness struck home!! A man who says he likes Koudou appears in front of Takashi…?!

A slightly different telling of the hit manga " Boku wa Tomodachi ga Sukunai." It still follows the same concept as making a friend making club. If you enjoyed the original you probably will like this.

A collection of one shot stories from Takako Shimura, the author of Hourou Musuko and Sweet Blue Flowers. These stories deal with issues relating to gender, romance, ideals of beauty, and relationships with parents.

1. He said "I'm a girl"
2. Rakuen ni Ikou (Let's go to the Paradise)
3. Shounen no Musume (Boy's Daughter)
4. The Theme of Akemi ver. Teruo
5. The Theme of Akemi ver. Yoshio
6. The Theme of Akemi ver. Haruo

7. The Flower
Contains the Transient Son character Yuki.

8. Sweet 16
A short, bittersweet story in which a girl realizes she's in love with her tutor, who's in love with someone else. The other main plot point is the main character's dread of the upcoming school marathon.

From Psycho Pandas:
A short 16-page oneshot about the relationship between two high school boys who are incapable of admitting their feelings to each other and the girl who perpetuates their anxiety.

Koyama Kei lost his mother when he was still in elementary school and never connected again with his distant, workaholic father. The only real light in his home life is his sister Moe: a bright college student who obviously adores him. But Kei has intimacy issues that even his sister can't pick up on.

At 15 years old, Kei's never been in love, but he has sex with anyone who shows him interest. While he's in someone else's arms, he can forget the void in his own life.

One day in late spring, Koyama discovers what's missing: a slightly spacey med-student named Fujii. Unfortunately, Fujii is his sister's boyfriend...

-DokiDoki

From ShoujoMagic:

Yori's attitude has changed. He and his twin sister, Iku, used to be inseparable as children, but lately Yori's been different -- eager to be apart from Iku. Iku worries that he hates her, but the truth is far more scandalous. Now, Yori would risk losing everything to have his little sister. Iku loves her big brother enough that she would never risk losing him, and so she'll do what it takes to keep them together... but Yori doesn't want to have her that way -- as a sister dedicated to her twin. Can Iku ever love Yori not as a brother but as a man?

Boku wa Imouto ni Koiwosuru received the Shogakukan Manga Award for shoujo manga in 2008.

From Neptise Scans:

Dracul's presence threatens humanity and the only ones who can stop them are the Exorcists, siblings bound by blood and granted the power to purge evil. The story centers around Vincent and Ryan and their struggle to become full-fledged exorcists.

After being told that his dad passed away, Souichirou comes back to the house which used to be his home 8 years ago. There, he finds out about the existence of his two older brothers - Masato, the eldest, and Kaname, the middle child. In order to receive rights to the house, Souichirou has to live together with them, and despite the chaos and arguments, it's fine by Souichirou if it means he can get the house. But one day, he accidentally sees Masato kissing Kaname...

From Storm in Heaven:

Russia, 1828. Natalia's family is fallen nobility, left poor by her father's chronic illness and mother's poor management. Her family's only chance at revival is her marriage to a wealthy noble. With her family's hopes riding on her future husband, what chance does a poor poet have at winning her heart...?
And the "poor poet" is no other than the famous Russian poet Aleksander Pushkin.

Mitsuki's a high school freshman worried about her looks--or, at least, her "baby face". Until, that is, she enlists a little help from classmate Atsuki and her makeup kit. When Atsuki's finished, the transformation is complete--and breathtaking. It's also when the romantic adventures begin--a roller coaster ride of the heart that young and old are sure to enjoy.

There are 2 extra chapters in 1/2 Ceremony (1/2 series book 4).

In the years following a great civil war between the Light and Dark Dragon clans. The Light Dragons are dwindling, reduced to hiding in small villages. The protagonist is Ryu, a young Light Dragon who awakens one night to find his home set on fire by Dark Dragons. After his sister is captured in the attack, Ryu sets off to rescue her. In the process, he joins a race to uncover seven mystical keys, before the Dark Dragons can use them to unlock a goddess of destruction.

When hanging out in a gay bar, Koushi Yanagi a university student, meets a very sexy office worker, whom after getting drunk accepts his advances. But when the office worker becomes sober, suddenly he loses his nerve, starts acting violently and runs away. Koushi disgusted and angry accepts an invitation from Takashi Kirishima, aka Ten, his sex friend.
At Ten's house Koushi meets the office worker again. He is Ten's twin brother, Arata Kirishima, a researcher in a laboratory. Later Koushi visits Arata's room when Arata is home alone. Arata denies the incident and tries to give money to Koushi asking him to leave, but Koushi offended, goes wild with anger and rapes Arata. Arata asks Koushi to keep what happened from his brother but it makes Koushi angry all the more. Blackmailing Arata with the promise of telling Ten everything, Koushi makes Arata his sexual slave, but gradually they become attracted to each other.

The plot revolves around an intranet-based online game (D.P. = Danger Planet) which is played using a V.P. (Virtual Puppet). VP is literally an avatar which a person uses in the game. However, unlike avatars (characters) from current online games, a VP is allowed to be modified (modded) by a person if he or she has sufficient programming skills.

Kilio Nimra, a normal high schooler who likes games. He and his friend Kurata always plays Danger Planet after school, one day they meet a very tough opponent.

From Tokyopop:
The discovery of an alien organic vessel submerged in the ocean reveals a plot to unleash planetary destruction... a collective of evil scientists called the Reclaimers works to hasten mankind's extinction. As one of Earth's defenders, Hime Utsumiya fights on a team of mecha called Brain Powereds to combat them. Unfortunately, the Reclaimers also have these mecha, and mankind's fate hangs in the balance.

In recent years, more and more girls are experiencing the development of "tertiary sexual characteristics" during the later years of their puberty -- that is, the rapid masculinization of a certain part of their external genitalia. Ooi Haruka is one such girl, who has until now kept the changes in her body a secret from everyone but her family. However, after an embarassing incident involving the guy she's been crushing on in a crowded train, she wakes up to discover herself at school, surrounded by a group of students calling themselves the "Bra Girls (Swing Girls)." And they know her secret!?

Boys Be... (ボーイズ・ビー Bōizu Bī) is a manga created and written by Masahiro Itabashi and illustrated by Hiroyuki Tamakoshi. Three different Boys Be... manga series were serialized by Kodansha in Shukan Shōnen Magazine. In 2009 Kodansha announced a fourth series, Boys Be... Next Season, starting in the November 2009 issue of Magazine Special.

From Tokyopop:

An anthology of stories about ordinary high school guys and their relationships...or lack thereof. Boys Be...takes a look at the trials of love and loss from a refreshing point of view and often adds interesting insight into what a relationship is like from an average guys point of view!

A collection of six short stories:

1. Blue Moon Lovers
Blue moon... a phenomenon so rare, it's almost a miracle... Without thinking, Yuri tells the super cool bartender Rukia that she's fallen for him at first sight. Rukia rejects Yuri outright, but that's not enough to make her give up...
- From Sunny Side Up Blog

2. Karefechi

3. Koi Shoku Neiru

4. Kodou ni Kiss shite

5. Ikenai Kareshi

6. Boyish na Kanojo
Ayame, a popular idol who looks like an Ikemen but is actually female, has to claim she has no lover. In actuality however, she is going out with a regular guy, Nanase. But keeping both her idol status and love life in harmony may be harder then she expected...
- From Intercross

From ]Nagareboshi Manga:

Hijiki (a girl with an unusual name) has just entered a new school, and on the way there she encounters a mysterious boy alongside a beautiful lake. Hijiki has some secrets of her own, and will this boy be able to listen to her silent pleas for help...?