Shoujo/Josei manga:
Basara
In a small village, twins are born: a boy, Tatara, and a girl, Sarasa. The prophet Nagi declares that Tatara is the chosen one who will free Japan from the tyrannical rule of the King and his four sons. But when the ruthless Red King slays Tatara, Sarasa must take on her brother's name and responsibilities and embark on a quest to free Japan and deliver vengeance to the Red King.
The Magician's Bride
Hatori Chise is only 16, but she has lost far more than most. With neither family nor hope, it seems all doors are closed to her. But, a chance encounter began to turn the rusted wheels of fate. In her darkest hour, a mysterious magus appears before Chitose, offering a chance she couldn't turn down. This magus who seems closer to demon than human, will he bring her the light she desperately seeks, or drown her in ever deeper shadows?
Chihayafuru
All her life, Chihaya's dream was to see her model sister become Japan's best... That is, until a quiet, unassuming transfer student named Arata tells her otherwise. A dream, he explains to her, is something she needs to work at herself. Arata plays a competitive version of a traditional Japanese card game--known as Hyakunin Isshu--in a way Chihaya has never seen before. After taking Arata's place in a game, Chihaya discovers she has a passion for it. Now Chihaya wants to become number one in the world, the Queen of Karuta.
Banana Fish
New York City, 1985. A dying man leaves gay gang leader Ash Lynx a strange drug, the key to something called "Banana Fish." The mysterious potion will lead Ash to a disturbed Vietnam vet who remembers a massacre - and into brutal battle with the mafia over control of the drug.
Orange
One day, Takamiya Naho receives a letter written to herself from ten years in the future. As Naho reads on, the letter recites the exact events of the day, including the transfer of a new student into her class named Naruse Kakeru.
The Naho from ten years later repeatedly states that she has many regrets, and she wants to fix these by making sure the Naho from the past can make the right decisions—especially regarding Kakeru. What's more shocking is that she discovers that ten years later, Kakeru will no longer be with them. Future Naho asks her to watch over him closely.
Hanshin
Conjoined twins Yudy and Yucy are as different as possible. Older Yudy is intelligent but ugly, as her nutrients are used up by her beautiful but simpleminded sister Yucy. Loving and hating so deeply, where does one girl begin and the other end?
A, A'
The story A, A' raises a troubling question: How would you feel if your lover died - and was replaced by a clone? Could you recreate your relationship with someone who was physically exactly the same but didn't share any memories of your life together?
In 4/4, teenaged Mori flunks out of an ESP training program. But when he meets Trill, a beautiful Unicorn, his latent abilities begin to blossom...
In X+Y, Hagio uses science fiction to explore questions of gender and sexual identity. Time has passed, and once again, Mori finds himself inexorably attracted to a member of the unicorn race - but this unicorn is male... and so is Mori.
Oooku
In an alternative timeline of feudal Japan, a strange disease that only affects men caused a massive reduction of male population, thus females have to pick up men's jobs, changing the social structure. Now, after 80 years of the initial outbreak and current man:woman ratio of 1:4, Japan has become completely matriarchal, with women holding important political positions and men being their consort. Only the most powerful woman—head of Tokugawa shogunate—can keep a harem of handsome yet unproductive men, known as "Oooku."
Koe no Katachi (this isn't shoujo, but the manga is so amazing I think you should read it)
Shouya Ishida, a boy always looking for ways to beat boredom, ends up looking for it in the wrong place. Weirded out by his new classmate, a deaf transfer student named Shouko Nishimiya, he deems her as the target of his ostracizing and bullying. Day after day, Shouya picks on Shouko, unaware of the effects of his thoughtless actions. He finally understands the pain he has inflicted on her when one day, his bullying culminates in her leaving the school, and his classmates begin to shun and harass him every chance they get instead. Determined to right his wrongs, five years later, Shouya, now a third year high school loner, meets Shouko again. Thus begins the story of a young man's path to redemption.