From Tokyopop:
From a small lake nestled in a secluded forest far from the edge of town something strange emerged one day: Three young girls. The three girls, Shem, Hamu and Japheth, are sisters from another world. Equipped with magical powers, they are charged with saving all the creatures of Earth from becoming extinct. However, there is someone or something sinister trying to stop them. While saving our world from destruction, these sisters live like normal human girls: They go to school, work at a flower shop, hang around with friends and even fall in love...

"Basara - The spirit of freedom which denies old authority, transcending traditions and customs."

Born under a prophecy that will liberate and unite Japan, Sarasa has had to take her brother Tatara's place as the "Boy of Destiny." Fighting for the oppressed, Sarasa journeys across Japan to gain allies and defeat her enemies--all while keeping her identity a secret!

Basara won the Shogakukan Manga Award for shoujo in 1992.

Collection of love stories:

1) Butterfly Cloud by ASHIHARA Hinako
N Island is a small island where all the kids know each other, and they're excited to meet the new transfer student from Tokyo. Fifth grader Kanta doesn't want it to be a girl, because his classmate Kyo is the only icky girl the island needs. In a way that makes Kyo happy -- because she's always known she wants to live out her life on the island as Kanta's wife someday. But the transfer student, Ritsuka, is a girl, and a shy one with a mother who's shunned by the island. So Kyo makes it her mission of good faith to assimilate Ritsuka, but then Kanta starts acting more interested in Ritsuka than in Kyo... When the main cloud splits into a butterfly cloud, which girl will be the one to separate from the rest...?
This story was released as a oneshot in Chouchou Kumo.

2) Racing Queen by IZUMI Kaneyoshi
When it comes to being a racing queen (it's like being a cheerleader for Nascar), you're either a bitch or a lost puppy. Ei learns this lesson the hard way from Akane, the reigning racing queen of the famous Meitoh Team, when Ei joins the team to put herself through college. It's only by doing harm to others that you succeed, and once you've succeeded, everyone wants to do harm to you. Ei's dream was to be the top racing queen, but once she gets there, it turns into her worst nightmare...
This story was released as a oneshot in Ni no Hime no Monogatari.

3) English Garden by SAKURAKOJI Kanoko
Hayato is moving to England in one month, so he approaches Fumio and tells her to date him -- almost like a command. He's dominating, stubborn, and selfish, and Fumio really can't say no. But Hayato isn't without his charm; he has a talent for making things grow, and he designed a gorgeous English garden. Now he wants to spend his last month in Japan building a garden with Fumio. As the garden grows and changes, so do its gardeners... and as time becomes strained, so do their emotions... This story was released as a oneshot in Baby, Star.

4) Pure White Anniversary by AYASE Riu
Just by selecting her, and saying her name, she became the class´ representative, and after time, trusted by teachers and students. That always maked her excited about working hard and being better. But, not all is white, not all is pure, when she was in trouble, A guy suddenly appears to help! Who is this guy? Why is he helping her? And, why does Sakura feels scared whenever she is with him? Well... we sure want to know.

5) The Coffee Shop that Ends Unrequited Love by ADACHI Keiko
This story is about a girl called Rui. She's always too late on dates. But when she met Shiyouta she fell in love with him an want to be not late anymore...

6) Great Waiters? by WASHIO Mie
At 175 cm, Eisei (real name Haruyo) never thought she would ever find a boyfriend because of her height and her rather tomboyish looks and demeanour. Under her friends' recommendation, however, a visit to the renowned 'Hot Cafe' caused her to fall for a charming waiter named Kono... who promptly dragged her to fill the vacancy -- as a male waiter?! Having a chance to get closer to him is one thing, but has Kono also accidentally mistaken her for a boy?! How is Eisei supposed to express her feeling for him now? With a cafe filled with handsome waiters and the pretty girls who swoon over them, this 'pretty boy' has work cut out for her!
This story was released as a oneshot in Kanojo ga Cafe ni Kayou Wake anthology volume.

Yuuki Kimino is a very boyish-girl who saves girlish-boy (and crossdresser) Izumi Junichirou from a train molester. Jealous of his "girl-power", Jun-chan agrees to coach Yuuki on being more girly in hopes that she too can be called cute. However, despite being a girl, acting and dressing like one might be a little tougher than she'd think.

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.

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!?

By anonymous:
Nohae has been crushing on Dona, his neighbor, since they were younger. Dona is a girl who was obsessed with money as a child and would make her childhood friend Nohae actually pay her. Time has passed and now she's a teen, broke and living on the streets with her dad. Her dad meets Nohae and arranges for Dona to live with him. But Dona's not your typical heroine. She's one of those fake people, maintaining a perfect image at school but in front of her parents she's self-absorbed, a glutton, and is quick to nab a meal or swindle money. She's quick to anger and has a grudge against Nohae, but he likes her so much he's completely unaware.

From StarryHeaven:

High school first year Sara has a secret…she’s really the super-popular singer SALA! However, as an idol her gender is kept a secret from the world in order to sell her music. But can Sara win when she wants to be just Sara…?

Jail: Risk Hunter number one! He can alter his appearance using "Kara" and uses it wisely to kick his enemies' ass.

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"Risk hunters" are professionals who handle jobs considered too tough for normal law enforcement, such as kidnappings, combating terrorism, and preventing murders. One man who stands above them all however is the legendary Chameleon Jail, who has the ability to manipulate his "kara" or internal human body energy in order to physically change his appearance into that of any other person.

Throughout the series, he pursues several assignments on behalf of various clients given to him by Shall, a woman who runs a detective agency in New York City. All difficult, the successful completion of these assignments hinges on Jail's ability to change his appearance when the time is right.

From Attractive Fascinante:
Yuu, Kouichirou, Natsume and Shino are classmates.

1-2) Yuu-kun's Love & Kouichirou-kun' Love
Kouichirou took really good care of Yuu since young. Yuu was afraid that Kouichirou would leave him behind if his grades dropped so he worked really hard and got a fever. When Yuu kicked up a fuss in the infirmary, Kouichirou kissed him. What did that kiss mean?

3-4) Natsume-kun's Love & Shino-kun's Love
Natsume and Shino had been sex buddies for quite some time. Although they had feelings for each other, they never confessed to each other. Shino finally broke down and confessed. Would Natsume accept him?

5) Light Whispers

What if the Meiji Restoration never happened? Bakufu still holds sway, the class system has never been abolished, and there is no westernization. The story is set in modern-era Edo, which had never been renamed to Tokyo, where people go to Kabuki for entertainment and hang out at pancake house. It centers around Sobi, the sister of an Edo magistrate who goes to school with Michisato, who prefers to be called Michel, the eccentric son of the ruling Tokugawa clan's Mito family.

Older cousin returns after six years to find his younger cousin has grown up really pretty.

In a not-too-distant future, the Earth has been overrun by a horrifying technovirus. Mechanical parasites, mistakenly created in an attempt to advance technology, attach themselves to human spinal cords and turn their hosts into cyborgs.

Desperate to rid themselves of this technological terror, the remaining human survivors must band together and learn to defend themselves against their android enemies.

One of the five handsome men in the incredibly popular idol group "Z", Riku, is actually a girl! She's tied with the leader, Touya, for popularity. She pretends to be the type of guy that makes all the girls smile and is extremely cool-looking. However, when she receives a Christmas present from Touya, she decides she wants to show him her feminine side...!?

*Includes a short story called Romantic Shiyo! (Let's Be Romantic!).

It happened after school one rainy day... A group of friends have stayed behind to prepare for the next day’s school festival. One moment they are idly telling ghost stories but the next an enormous earthquake strikes and the entire school seems to fall down around them. They awake to find themselves trapped in a parallel version of their school. A school abandoned and disheveled and whose calendar dates back to 1927. Can they find a way out of this nightmare or are they doomed to the same fate that befell the other victims whose corpses that lie numerous throughout the school?

Akane has a crush on the princely Yuu, but when she finds out he's living with super attractive Kei, she makes a deal with the other girl to move out of Yuu's house. But Kei insists on moving in with Akane, and is now running her ragged with demands! Will Akane get any chance with Yuu or will all her time be spent with Kei?

Sequel to Divine Melody. Caisheng, the half demon fox god who can change gender at will, wanders the Earth looking for her lost lover's reincarnation, Wei Tzequi. Wei Tzequi, a former divine being, was banished from the heavens for breaking the rules, but Caisheng refuses to give up hope she will meet him again.

But finding Wei Tzequi is only the start of Caisheng's troubles. Other beings, both demons and gods alike, want her for their own reasons. Some see Caisheng as the salvation for their own race, while others want to kill her for their own nefarious purposes. Even a fox-god from the heavens, Yuer, finds himself intensely curious with Caisheng, and decides he will take her back to the heavens in order to marry her. In order to survive, Caisheng must muster what allies she can so she can continue to wander - and find the one person she has spent so many years seaching for.

From Transcendence:

This is a tale full of wonderful Ancient Chinese legends. A group of beautiful female fox demons lived at the base of a mystical mountain. Among these foxes is the very special Caisheng, a little fox girl with the ability to change into a male fox demon when she matures and allow the continuation of her species. One day, she secretly went into a nearby human village and befriended a boy named Duoxi and a girl named Xiaoque, and when the little fox child is attacked by a dog, the two human children saved her! Now the two children are marked, and will remain so -- even in their reincarnated lives -- until Caisheng repays her debt to them...

Two hundred years later, Caisheng not only becomes the most powerful fox demon but also has mastered the art of gender transformation. She begins her search for her saviors' reincarnations: the boy now known as Yunshi, and the girl as Ping'er. Not knowing Caisheng's true identity, Yunshi falls in love with the female Caisheng, and Ping'er with the male Caisheng! But Yunshi is a priest whose duty is to destroy all of the demons... what will he do when he discovers Caisheng's true nature? And whom will Caisheng choose in the end?

(Clarifying note: Very low smut content)

What does gender matter? And why do we accept the social frames that are forced upon us? These questions are taken up when Maho, a male-to-female transsexual, saves Fujiko, a girl from a rich family who's left home and is living on her own, one night, and the two become fast friends.

Satomi wakes up late one morning and starts running to school, but she crashes onto Keshi. They both stare at each other for a moment and noticed they switched bodies! Now Keshi is in Satomi's body and Satomi is in Keshi's body. They have to continue the other's life until they fix their problem. But things get complicated when Mariko, Satomi's best friend, confesses that she likes Naoshige to Keshi, in Satomi's body, and he doesn't know what to do. Includes two other stories: • Mushibana After graduating from middle school, HIRAI Yuka hopes to gain many new friends and a handsome boyfriend in high school. But during her days before entering high school she manages to get a major tooth ache which totally ruins her class introduction and kills her chances of gaining new friends and boyfriend. Forced to go to the dentist and feeling like her life couldn't get any worse, she makes a chance meeting with a bishounen, Yuuki Yuuta-kun at the dental clinic, Yuka's life is suddenly starting to look better!? - Intercross • Tomodachi Sando