From Ivyscan:

Karin and Lisette are witches who trained together when they were younger. After a long absence, Lisette has moved to a nearby forest and seems to be stealing Karin’s customers. Karin really wants to see her old friend again, but she can’t seem to get past Lisette’s apprentice, a young man named Ruin…

Volume 1 Oneshot: Meeting Place
About a student that can't say thanks to her overly enthusiastic teacher; so, she is thrown back in time to figure out that she still can.

Volume 2 Oneshot: Mission Sachiyama
About an after school program that trains modern day ninjas.

Reiji and Kasuga head out to Tokyo to become the "Gods of Rock," but they seem to always attract trouble. On their way, Hayama Ryo and Fujii Ran join them in their quest.

From Wataame Shoujo:

The story is about Kobato going to Japan to find her brother but accidentally, she becomes an idol when she meets Takeru. The catch is, Takeru and probably everyone else thought she was actually a he because of how she acts and dresses.

A very short story (3 pages long) about a boy who transform into a girl to become a hero, but she has to collect stamps to be a real hero.

Yona Ryouma, a normal high school boy, saves a man from another world at the cost of his own life when a mysterious earthquake occurs. The man, Emillio, uses a potion which apparently saves Ryouma's life. However, he is also changed into a girl in the process.

Emillio is actually the prince of this alternate world and he declares Ryouma as his wife, presumably on the context of saving his life. But what about Ryouma's life as a high school boy in his own world? And will he come to accept being the prince's wife?

Yukinari Takase is a huge masochist who instantly takes a liking to Rion Tachibana, a menacing trap who just transferred into his class. After Rion believes Takase has uncovered his secret, he decides to make Takase his servant in order to keep his mouth shut.

Note: Because Shinjo Mayu stopped her job relationship with Shogakukan, she continued her incomplete manga in Asuka and called it Ai Ore! - Danshikou no Hime to Joshikou no Ouji This can be considered a continuation of Ai (w)o Utau Yori Ore ni Oborero! or even as a second series.

In this screwball romantic comedy, Haruhi, a poor girl at a rich kids' school, is forced to repay an $80,000 debt by working for the school's swankiest, all-male club--as a boy! There, she discovers just how wealthy the six members are and how different the rich are from everybody else...

Includes 4 chapters of the story "Romantic Egoist" in various volumes, starring a pair of twins who play matchmaker with their fellow students, teachers and the like.

This is a 4-koma comedy about a young girl named Ichimatsu Kohina who got possessed by a low grade spirit called Kokkuri-san.

Masago is an average student. Everything about her is average except for her older brother, Shirou. He's the president of the student council and everyone admires him. One day, while walking home with her brother, they get into an accident and her brother dies saving her. After Shirou's funeral, Masago goes to the house of her brother's best friend, claiming to be her older brother.

Keitarou Itsuki is a junior high school student unhappy about the menacing look of his eyes. Keitarou tries to confess to the girl he likes, Aoi Tokujira, but she rejects him flat out. Thinking that his eyes were the reason why she rejected him, he confides in his older sister about it at her salon, who helps by giving him a complete makeover...as a pretty girl! Forced to head home like this, he runs into Aoi in town, but she doesn't recognize him and thinks he's a somewhat manly girl. Before he can leave, Aoi asks him to help her overcome a problem she's had for many years: an intense fear of men.

A collection of short stories. Note that the vast majority of these stories contain heterosexual romance themes. A few stories explore transgender issues, but it's a stretch to call them shounen-ai or BL romances. This series demographic is josei.

Le théâtre de A
1.Oeufs D'ange - Tenshi no Tamago
A man is asked by a young painter to be her model.

2. Velvet Going Underground
A doll becomes a super idol. Hijinks ensue.

3. Childhood's End
Alastair runs away and meets the Rabbit.

4. Bite Me Something
Allistaire followed Mr. Rabbit all the way to Wonderland. Will he be able to find him among the crowd?

5. Long Along Alonging
A girl asks a vampire to be his apprentice. But what is her motive?

6. Till Dawn
In a dark tower, a caged voice is singing until a hunted man enters the darkness.

7. Leçon un
Sequel to Long Along Alonging.

8. My Skin on My Back

9. Highland Walker
Sequel to Leçon un.

10. Perfect World
The story of a young wife whose husband is infected with a fatal disease called Flower-Blossomitis.

11. Perfect Lady
Sequel to Perfect World and drawn especially for this book.

12-13. Looks Like a Teaspoon
A boy named Allistaire is often teased at his all-boys school. One night he dresses like a girl and stumbles upon the boy who often bullies him, Simon. Allistaire runs off into a tower and as Simon runs after him, we see the sign "Welcome to Wonderland" hanging by the tower's door.

14. The Pearl Blue Story
Do you believe in mermaids? Coggy, a young boy finds a mysterious lady laying down near the shore of the beach. He brings her home to help her.

15. I Am a Piano
A piano tells the story of her life and the people she encounters.

16. Parade

Le théâtre de B
1. Noël
A short story about a holiday romance.

2. Teddy Bear Satsujin Jiken (The Teddy Bear Murder Case)
Four murders have taken place at an all girl school. Lying beside each of the victim was a teddy bear with one missing limb.

3. Yonshimai Satsujin Jiken

4. A is for Alice
Alastair, a grown man, is off to follow the Rabbit once again to return to Wonderland.

5. Nedai no Musume Atelier no Musume (The Bedroom Girl, The Sculpture Room Girl)
A story about a girl in her death bed finding another chance in life in the body of a doll.

6. B&W (Black&White)
A story about a boy waiting for his sister.

7. Le Jardin du thé (The Tea Garden)
A mysterious story about a poor young man who orders a kind of tea called Huan Ying – “The Illusion”.

8-9. Free Fitting for Her
A priest and his captured vampire must save a naive and selfish young girl from the murderous desires of a Lolicon. But perhaps this girl isn't all that she seems.

10. Rose Dusk, Pale Moon

11. Hello, My Sister

12. The Happy Prince

13. Welcome to Wonderland
Simon, Alastair's old classmate, is now a grown man who bumps into his childhood Wonderland traveller.

The 15th Hierarchical City of Torifune is best known as the Military Academy for the NOL. There, future librarians train and hone their skills for whatever challenges may await them outside. The story centers around Mai Natsume, a girl who had just arrived late due to a week absence, but there seems to be several phenomena centering around her that could be more than just coincidence.

One day, a mysterious box arrived at Matsuda's door steps. The content of the box was none other than an android girl that insists that she's Matsuda's younger sister. Now, the purely otaku Matsuda has the privilege to live with a beautiful and submissive android sister that bows to his commands, or at least he wishes that were the case.

A tale of mystery and magic. Naito and Yuta Fuuga are twin brothers with very different personalities. While Naito is elegant and good in school, Yuta is athletic and often winds up in fights. Despite this, they maintain a close relationship. When their father turns up missing, both must travel to Dubai in search of him. A mysterious peddler has other plans though, as the twins soon find themselves in the world of One Thousand and One Nights.

On her death bed, Kousaku Sakamoto's mother tells him that after she dies, he should go to Tokyo where he'll be taken care of by her friend Ibari Oozora and his family. Since his father died three years before and with no where else to go, Kousaku decides to go along with his mother's last request. However, he soon discovers that Ibari is the boss of the Oozora Group mob ring. Uneasy about his predicament, he considers leaving, but he has second thoughts when he meets Ibari's four daughters–Tsugumi, Tsubame, Suzume and Hibari–only to find out that Hibari is actually Ibari's only son. Now Kousaku must not only cope with living among mobsters but also with refusing Hibari's advances toward him.

Our heroine is girl named Hina-chan. She is in her 20s. Hina has a handsome boyfriend now, but she will always remember her first love, a boy named Itsuki. When other kids would tease Hina, calling her ugly, Itsuki would defend her, and try to cheer her up and make her feel better. He and some of his family eventually moved away, leaving Hina heartbroken. But the memory of her first love will always make Hina feel nostalgic and happy inside. Itsuki’s grandmother still lives next door to Hina, so she still has a connection to him, somehow.

One day, Hina has a dream of Itsuki, and she is feeling especially nostalgic about him. She is just mentioning her dream to his grandmother, when they are interrupted by the arrival of a stranger. It is a tall, beautiful woman. Wait a minute… it’s Itsuki! Itsuki is not joking, either. She explains that she is really a woman on the inside, and now she is dressing that way on the outside.

Hina finds herself falling in love with Itsuki, regardless of Itsuki's gender. But Itsuki is only attracted to men. Will Hina end up heartbroken all over again?

Assassins--they are humans that have exceptional skills which they use in killing people. The most dangerous among them is the Assassin of Crimson--the former leader of the Assassin guild Yuuyami, and the one who killed the country's leader, King Mars. Due to this, the country's princess has declared that whoever captures her will obtain fortune and become the princess' husband, essentially becoming the next king.
Virgil is a guy who has red hair and looks like a girl. He is travelling with a performing troupe while searching for his twin brother Serge. His peculiar features seem to have matched the known characteristics of the Assassin of Crimson. The following events will lead him to discover the mystery behind the death of the king--and the identity of the Assassin of Crimson.

Simo Häyhä, the legendary sniper who distinguished himself defending Finland from Russia in World War II, is a woman.

From Decadence:

Mishima, a student at a school in the countryside, is bullied by his classmates. The reason is because he's seemingly gay. In reality, Mishima does like guys so he doesn't resist their bullying, and instead, finds solace in secretly cross-dressing. One day on the rooftop, Mishima finds the lipstick he'd lost before in the hands of Kirino, one of the bullies... and Kirino was about to put on the lipstick that Mishima used on his own lips. This is the story of young boys looking for a place they can really be themselves...