From MangaHelpers:
Kamiya Hiroki always thought women had it easy.
This thought was throttled by the fact that his 24-year-old sister does not work and plays games all day. Why couldn't he have it this easy? He wanted to become a woman and be lazy like his sister.
After blogging about his rants about his sister online, a mysterious reader comments on his blog, stating that there are ways to swap bodies with others. This would bring Hiroki's dream of becoming a woman to reality . Unfortunately for Hiroki, swapping bodies had unintended consequences when he returned to his own body.

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.

Elna was entrusted with ruling a country at a very young age when her father, the king of a small kingdom, fell very ill. With such a heavy burden placed upon a mere teenager, the king gave Elna an important piece of advice about how he made his time of rule a success: find your shadow. By finding her double, she will find the will to live and be brave even in the most dire situations. Elna does find a person who looks identical to her, but it turns out fate loves to play games. Teshio used to be a simple peasant who had a problem of always being mistaken for a girl but he is about to go from rags to riches because he becomes the new shadow for princess Elna.

From Viz:

The comedy starts when the cross-dressing begins! The Kobayashi twins, Mego and Mitsuru, were named after historical figures, but only Mego has grown up with a taste for history. So when Mitsuru is in danger of losing his weekends to extra history classes, he convinces his sister to swap clothes with him and ace his tests! After all, how hard can it be for them to play each other?

But Mego can’t rely on just her book smarts in Mitsuru’s all-boys, delinquents’ paradise of a high school. And Mitsuru finds life as a high school girl to be much more complicated than he expected!

Mireille is the daughter of a bakery owner and her twin brother Fred was adopted into another family when they were kids. One day a letter from her brother arrived, saying he was in love with another man's woman. She replied, challenging him to be a man and claim the woman as his.

Two months later, a beautiful young man named Richard, claiming to be a messenger from Fred, visits and tells her "I've come for you." When the bewildered Mireille resists, he proceeds to kidnap her! It turns out that Fred has eloped with the crown prince's fiance, and it is now her responsibility to impersonate Fred - the former Count of Bernhardt!

As a child, Yashiro Nonoyama developed an intense fear of men due to boys constantly bullying her. Now in high school, she dreams of being reunited with her first love: a girl who protected her one day from her bullies. Yashiro is in disbelief when a transfer student named Mikoto Saionji arrives who looks a lot like her first love, but she later discovers that Mikoto is actually a guy, and that he was her first love. Yashiro learns that Mikoto is rapidly turning into a girl, and the only way to counteract this change is for them to passionately make out with each other every day.

For her brother Subaru's sake, Hitomi decides to take his place at an all male prestigious high school for a year until he recovers and is discharged from the hospital. She gets to the school and runs into a few strange guys on her first day, but as soon as she tells them her name - they are surprised and make her go to the Lion Club. Hiding the fact that she's a girl will be difficult enough and now she has to deal with this strange group who are forcing her to join their club because they all believe that in their past lives they were members of the Shinsengumi!

Description by LuffyNoTomo

From the master of love comedy manga, Wakabayashi Toshiya, comes a high school fairy tale about love☆!

Shindou Rei (Cinderella) comes from a very poor family. Her only clothes are hand-me-downs from her brother, even her school uniform. So everyone always mistakes her for a boy. Even her close friend Hakuba Ouji (white horse prince), who starts developing confusing feelings toward her all the while believing she's a boy. Tsukumo Yuki (Snow White) is the leader of a delinquent gang and falls in love with Rei at first sight, also believing her to be a boy.

A 30-year-old business man makes a wish to be a girl. A chanting object runs toward him, and the next thing he knows he has became a loli elementary school girl.

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.

Isao Komori is a college dropout who spends his days cooped up in his apartment playing video games and masturbating. The highlight of his day is visiting a convenience store where an angel-like high-school girl called Mari visits every night.
One morning Komori wakes up in Mari's body. Another "Komori" inhabits his old body, and Mari has disappeared. Komori struggles to maintain Mari's ordinary life and starts to investigate Mari's disapperance. Perhaps Mari wasn't so innocent and perfect after all?

This manga is set in the Western Xia state at the beginning of the 13th century, when there were violent, ongoing incursions by the Mongol army. Guided by Suzuki, a student who has transferred from another school, a present-day boy called Sudo, a high school student who has been plagued by a vivid dream of a battlefield, is reborn as Shutohel, a female warrior for the Western Xia army, who has lived for vengeance on the Mongols, and travels to the battlefield. At the same time, the Mongol prince Yurul defies his own army, which is trying to destroy the Western Xia script, and makes plans to protect a collection of Western Xia writings. This is an epic, long-form action manga featuring elaborate, dynamic depictions of combat and the enigma of an ancient script.
Note: Won the 16th Tezuka Osamu Cultural Prize's New Artist Prize in 2012.

IS (Pronounced Aiesu in Japanese) is not your everyday manga. This manga strictly deals with cases of intersexuality. IS stands for Inter Sexuality. This manga deals with very serious issues concerning intersexual people. The pain they go through, the troubles they confront, and ultimately their inability to reproduce and even find a partner who will accept them as they are - It's all there in a form of manga. The series is consisted of cases, each dealing with different people - although some cases are much longer and more dramatic than others. The first volume is about the case of Hiromi and the case of Ryoma. The third case is of Haru and characters related to him. If you don’t know what intersexuality is, refer to the Wikipedia on Intersex.

From Kodansha:

Class troublemaker Ryu Yamada is already having a bad day when he stumbles down a staircase along with star student Urara Shiraishi. When he wakes up, he realizes they have switched bodies—and that Ryu has the power to trade places with anyone just by kissing them! After figuring out the workings behind this new and amazing ability, Ryu and Urara take full advantage of the situation to improve their lives. But with such an oddly amazing power, just how long will Ryu and Urara be able to keep their secret under wraps?

Mizuki gets confessed to by a boy in front of a special Mirror. Legend has it, that if you confess to someone you like in front of that mirror your wish comes true.
There is a slight Problem in this Equation: Mizuki is just a very feminine looking boy.
Also it seems that he caught the Attention of the Norse Trickster God Loki while glancing into the Mirror. Loki decides out of boredom to mess with Mizuki and turns him into a real Girl.

The world which was ruled by those called the descendents of god and had unique abilities: Heuk's (Black) clan and Sahwa's clans.

One day, Heuk's clan was destroyed by one of the average human clans, the Parang (Blue) clan. The Sahwa clan sends their heir, Gayeon, as bride to the Parang clan's heir as a sign of obedience.

But the one who's actually sent is the the heir's twin brother, Jayeon. Now, Jayeon lives amongst the Parang clan....

From Easy Going Scans

What happens when you take a good, long look and realize that your boyfriend is prettier that you? And what happens when you go to a high school with so few girls that you're considered a goddess? But then again, your pretty boyfriend is also attending the same school...

The impossible happens in 15th century Korea.

A princess who was disguised as her dead twin brother by her mother became king. Once her true gender is found out, the female king is sentenced to death by drinking a lethal dose of poison.

This story details the events of that forgotten king's life.

From MangaHelpers:
This is a story of a group of college-age people who struggle with gender and sexual identity.
Yuki (nicknamed Yoshiki) is a girl, but she is terrible at 'being feminine.' She mostly dresses like a boy and is often mistaken as one. However, she has to wear a skirt and imagine being dominated by a guy in order to masturbate. Nagao Mikako seems young and innocent, and she uses that apparent innocence to sell her body as a fake 15-year-old. She knows her youthfulness can't last forever, but she enjoys tricking the men. Her friends have no idea of her sexual habits and believe her to be sweet and sheltered. Aiba Kaito is a pretty good-looking guy, but he wants to be Nagao Mikako. He often dresses as a girl, picking out clothes that mimic Mikako's style. Though he's into cross-dressing, he is still attracted to women. Will these young adults and their friends be able to handle their 'guilty secrets' and muddle their way through this confusing period of their lives?

In a country where women rule supreme lives a poor but happy boy named Albert. An excursion to the city turns dangerous when he and his friend are abducted by slave traders, and later purchased by a noblewoman's servant. If this wasn't crazy enough, it turns out Albert looks exactly like the noblewoman who purchased him. But she's no ordinary aristocrat. She's a princess! And he's to act as her double from today on!?