[From Hanashi (Yaoi)]:

Ever since he was a child, Ryou has always looked very feminine. One day, a couple of girls from his class force him to put on make-up and to wear a girl's uniform. While he was walking around, he meets Kazuaki, who immediately takes interest in him and simply refuses to believe that Ryou is actually a boy.

Also contains BASIC OF BASIC and Fleeting Foam, two unscanlated, non-BL stories.

Arimasa was a half-demon priest who cared nothing of what others thought of him. That was, until one fateful night, while on a mission to exorcise a gang of demons, he encounters Kagetsu, a clumsy cat demon who will eventually change his world, and more importantly, his views of it.

A maid cafe with boys done in a 4 koma format

From Enchantment Scans:

Farewell, my manly side! Ayase Natsu, with the goal of becoming more ladylike and popular, enters the prestigious girl’s boarding school. On the first day in the dorms, Natsu finds out a secret about her roommate, Konno Fujio, who is Natsu’s ideal model of a girl. How will Natsu react...?!

A collection of oneshots about unusual couples: including one that comes together through the uke's love of late-night flashing, crossdressing and lacy undergarments.

1) I Like Every Part of You

2) Love Squared

3) Love me some more! (Motto Boku wo!)

4) The Depressed Don Quixote
Hijiri and Kunihiro are in love and dating, but Hijiri is starting to worry that their relationship is just a sexual one. All of their dates end in the same way, with sex in public places! Maybe if Kunihiro was jealous Hijiro could find out how he really feels...

5) Dangerous Dreamer

From NetComics:

A pulse-quickening tale of swords, sorcery, far-away kingdoms, and the fairest princess in the land... with a twist.
When Prince Jed's bride-to-be, Elena, elopes two days before their wedding, her desperate family dresses up their youngest son Nicole and sends him to get married in her place. With his beautiful blue eyes, flowing blond hair and strategically placed apples, nobody bats an eye at the pretty young 'maiden' standing before them. But how long can Nicole keep up this charade? Despite the odds against them, the two princes share many adventures and intimacies in this mesmerizing romantic drama.

Note: There are both romance and shounen-ai pairings in this story.

Web Publication
English Publication

From DGT: When Asano Arisu was little she was badly bullied by the local boys, now a high school student she's famous for her vehement hatred of men and boards an all girls school. When stunning Fujimi Kira enters and becomes her dorm-mate, proclaiming that she also hates men, Arisu thinks that it must be a fated meeting. However, they both have secrets that they need to keep from the Dorm Head, strict Kamitani-Sensei: Arisu keeping a pet ferret in the dorm, and Kira the fact that she's actually a BOY--much to Arisu's horror. It appears that he's at the school to uncover the mystery of his older half-sister's supposed suicide 2 years before. Will Arisu be able to cope with having to share a room with a boy, let alone help him with his investigations? And just how dangerous will it be to solve the mystery?

Yashi has wandered with her father for fourteen years, and only now has she discovered that her own mother is actually Bocinia’s current queen. To see her mother, from whom she was separated when she was just an infant, she and her father enter the palace, but she never thought she would accidentally run into the Princess of Bocinia, and then become her bodyguard by mistake...

NOTE: This manhua ends at Volume 4. The continuation of the story was written in a novel.

From Rosa Negra:

A Prince Charming suddenly appears in front of a country girl on a remote island.
"I love you, I want to be happy with you like this forever."
Setting a foot on a strange city to find her Prince Charming, she finds out that he is actually the Entertainment Industry's top star, Gang-Woo Choi.
Even after seeing her, he pretends as if he doesn't know her...!!!
"Gang-Woo Choi! You dare play around with me? I'll never forgive you!"

Aizen Kanou, just like any high-school boy, yearns for a girlfriend. But he's so painfully shy he flees when any girl tries to talk to him. Except his childhood friend, Yuzu, who scolds him for being so shy. But she leaves behind a temple love-charm.

That night in his room Kanou uses the charm to demand heaven grant him his wish for a beautiful girl. When he wakes up in the morning, he finds his wish has been granted--and the beautiful girl is himself.

From Awakened Memories and Covenant of Darkness: My private tutor, Midorikawa-sensei is a student attending a super elite medical school. He confessed to me and we started dating but I inadvertently lost my virginity! It is because, everyone around me already experienced their first time and I thought it was too late for me. At that time, my non related sister who has always lived separately from me returned. We met for many days and suddenly she is a he. A he who wants to have a romp in the hay with me!?

A collection of mildly ecchi otokonoko-styled stories focusing on crossdressing high-school boys and the boys who like them, mostly from the men's magazine Oto Nyan. Some of the stories are continued in Hiriajuu Shuudan ga Classmate o Josousasete Kanojo ni Shite Mita.

1-3. Raising Decoy
A boy helps his classmate go undercover in drag to catch subway gropers, and finds that he looks disturbingly good in a dress....

4. Ato no Matsuri (retitled Spilled Milk in the English edition)
A group of male students, having failed to get girlfriends, are becoming desperate; what will these "innocent" boys resort to?

5. Tenshi no Houbutsusen (Parabola)
Baseball-themed romance short.

6. Actress
A boy joins his high school's film club to meet the actress from their amateur film, but gets a surprise...

7. Shishiza no Boku to Natsu no Yozora (retitled Leo and the Night Sky of Summer in the English edition)
The president of the school astronomy club wants to catch UFOs.. maybe some "sexy female alien" costumes will help?

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.

From MangaHelpers:
Sakurai Seri wants to be an idol, but he's so nervous that he seems to only meet with failure. Then, one day, he and two other boys are chosen to debut as members of a new idol group, "Otoko no Ko." The other two boys are the cool, serious "Ren" and the enthusiastic, cute "Tama." The only catch is that they plan to be a male idol group that dresses as girls. This may be Seri's big chance, but he never imagined himself as a female idol.

From Tokyopop:

In a private school only recently open to girls, flower-lovin' Takaaki is a breath of fresh (and gender-blurred) air! Having to room with the stone cold Sonoh Takahara has certainly caused him some angst, but don't fear. Sonoh's twin is his complete opposite, making for a whole mess of fun filled with cute boys and silly misunderstandings.

Mika has a special relationship with an abused girl who has an extreme fear of men.

Beautiful, delicate Yoon Sul and tall, brawny Taehee are exact opposites, and yet somehow they can't escape each other! And now with the addition of the popular student representative, Sijun, being interested in Taehee, how will Yoon Sul react?! Action-packed romantic comedy with a twist!

Takatou Iori, a high school ninensei, while on his way to school to confess his love to classmate Kusanagi Mikuru by means of a love letter, gets ran over by a truck to save a cute elementary schoolgirl.