From Divine Sanctuary:
Sapphire was supposed to be a tomboyish junior high school girl who's not interested in boys, but it all changed on her 14th birthday. Not only did she find out that she's prince Sapphire, the Ribbon Knight, but she also has to protect a country called Silver Land!?
Based on the original work by Tezuka Osamu.

Glen and Linus are orphans training to fight for a country on the losing side of a war. Glen has a secret that only Linus knows. Will Glen's secret stay hidden? And what exactly is Linus hiding?

A boy wakes up to discover he has become a girl! How will this affect his daily life?! A new one-shot by the award-winning author of Fire Punch, Fujimoto Tatsuki.

"What, isn't it fine to cling to you? As fellow models and girls." - "No... Though we're both models and girls... buuuut (>_<)"

Hinako has been a successful teen model for several years, when suddenly a new rising star appears: Mashiro Yuu. Cute, innocent and feminine - how can Hinako stay at the top of the fashion world? But what if the newcomer isn't what she seems to be..?

When his twin sister dies, a young boy decides to confess to the man he likes, but with a strange twist.

A collection of oneshots:

From A Willful Muse & Alice Dreams:

"Wanna book a room with me?” It was only meant to be some harmless teasing! Aoi’s never even had a first love but now a mysterious boy has accepted her joking offer seriously. From a misunderstanding, Aoi and the boy start a passionate relationship. It’s only physical, right? Or has Aoi unconsciously started to fall in love with him?

- Tengoku No Tsuki - At an all girls school, Yuuri is the idolized, boyish and tall, upperclassman. With rumors of the "Perverted Hand" flying about the school, what will Yuuri do when her best friend is the next victim?

- (Chapter 3 continues Tengoku No Tsuki) Protecting Eien's secret and granting his happiness is Yuuri's main focus of her beloved. But how will Eien react to the Priest getting too close to Yuuri during the school play?

- Vampire Lover - Saku Mikuriya's parents divorced and she was left to live with her headmistress grandmother. As she cried of how she was unwanted, a man with golden hair and golden eyes appeared before her. "Then do you want to leave with me?" he offered, they made a promise when the flower blooms, he would come and take her away. 10 years have passed and the flower only buds, but what happens when a mysterious transfer student arrives and he looks exactly like the man she met 10 years ago?

- Nana is ordinary, plain, doesn't stand out, and totally in love with Shu Aiba, a model and her classmate. What happens when Shu picks her to be his "girlfriend" for his "Tropical Island Vacation with My Girlfriend" shoot?

N/A

From Viz:

Megumi Amatsuka, a rough and tumble nine-year-old boy, always dreamt of becoming the "manliest man on earth." Upon receiving a book of magic from a sorcerer whom he saved from a group of local thugs, Megumi summons a genie in order to make a wish. But due to a sick twist of fate, the genie turns out to be an evil one, and Megumi winds up being the "womanliest woman on earth"! Six years later...Megumi is the most desirable girl in school, but deep within her hot-mama façade is the same trash-talkin', punk-stompin' boy.

From ShoujoMagic:
There is a legend in the kingdom of Paros -- a legend of the Sword. It is said that if one who is unfit to rule should wield it, it will mean the ruin of the kingdom. As sole heir to the throne of Paros, Princess Erminia must accept the Sword and a husband when she comes of age on her next birthday. But the princess refuses to wed any man who is less of a man than she -- which excludes every man in the kingdom! Just when Erminia is ordered by her father the king to wed her foster brother Yurias, she has a fateful encounter with the unfortunate, beautiful maiden Fiona..!? "The Sword of Paros" is a miraculous romantic fantasy about defying convention, transcending gender and status, and knowing oneself.

Everyone’s pleasure is catching...

Hiiragi Hayato, a male high-school student, has no choice but to submit his body to pleasure, to the stimulations from other people’s sensations.

He has an ability involving the body that is too strong to be called a delusion. As he encounters a cat in heat, the stimulation from the cat will...
When he sees an av actress, then the pleasure of the actress will also...

The pleasure that can be attained within only 5 seconds is a secret only for Hiiragi ♡

Hiiragi takes pride in having a masturbation life that anyone would be jealous of.

However, such covert enjoyment is found out by his childhood friend, Terada Tsukasa.

With the pleasure that cannot be controlled, comes the thrilling psychic love that sways both body and heart.

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.

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.

Shun Hayasaka is a cross-dresser in high school who secretly enjoys posting pictures of himself in drag online. This earns him several fans, one of whom is Yasuda, a 32-year-old man suffering from depression who has trouble communicating with others. After they meet up in real life and start having sex on a regular basis, Shun is unsure what to do when Yasuda starts expressing more interest in him than just as a sexual partner.

From CMX:

Will a half-mermaid, half-human girl bring an end to the feud between humanity and the mer-people — or bring about the destruction of all life on Earth? As a merman named Shona is returning to his birthplace to spawn, he meets a young human, Jimmy, who suffers from amnesia. Together, Jimmy and Shona set off to find the missing girl. Will they be able to avert a mysterious prophecy, or will finding the secret of Jimmy's identity delay them enough to set Earth on the path to destruction?

Model student Daisuke Mizuki has a secret swimsuit fetish. What will happen when he gets caught taking pictures of girls in swimsuits by his teacher!?

A meeting on the bus to the underworld. Fate… Responsibility… To face it all or to run away?

High-class Robotics School a.k.a. Kousen is a high school that professionalizes in robotics. Although they have won many robotic competitions, they are not very well known for anything. The story doesn't focus on the school itself, but revolves more around a boy named Kaneko and his misfortune in the school. He is forced to cross-dress and do various "things" throughout the school year. No one knows what will happen in this school, especially when the senpai are a bunch of perverts!

From Tokyopop:
Through a series of coincidences, Yoshinori wound up having to fill in for his beautiful older sister as a model for a bridal gown. Now, he has discovered that he has a liking for cross-dressing, and that by doing so, he is learning a great deal about what it means to be a woman--and a man.

Contains a short story entitled "Reason" in volume 2

1-4) A gardener and a phantom thief steal the heart of a lonely rich boy.

5) A little dark story about a host and a beautiful male prostitute.

Sou Kagura is enjoying his life as a new high school student until one day when his parents abandon him due to a large debt they had amassed. To get rid of their debt, they essentially sell him to Mikoto Ouzuki, a wealthy land developer who wants Sou as his sexual pet. However, Sou's older sister Ui intervenes with a proposal: If Sou can pay back the debt in one year, he's off the hook, to which Ouzuki agrees. What Sou only finds out later on is that Ui's plan is to open up a maid cafe with him as one of the maids under the name "Kanade".