In the story, the main character is on the way back home from being rejected by a girl when he finds and picks up a high school girl who has been abandoned on the roadside.

From MangaHelpers:
At school, Kamazaki Yuu feels as though there is a circle drawn around her, a line that no one will cross. A part of it is because her face looks mean, and another part of it is because she's rather socially awkward, but the largest part of it all is that she has earned a reputation for being really bad-tempered and violent to the people around her.
This all changes in her second year of high school.
The cute, friendly, and popular Kume Asami one day inexplicably crosses that invisible line and decides to be her friend. Kume introduces "Kama-chan" to friendship and to the 5-man futsal club that meets on the school roof. As Kama cautiously enters Kume's club, she may find herself able to grow past the bad expectations people have of her, and enter into a new, happier, high-school life.

A deadly virus is spreading across mankind, turning humans into gruesome monsters known as ‘Kanshu'. Yet no one knows of their existence, except for the organization called ‘F.L.A.G.', dedicated to hunting down and destroying the source of the infection. Its members possess extraordinary powers, capable of unleashing righteous fury on their enemies.
One day, a cell phone message from a dead relative leads estranged youth Riku Amami unwittingly into the conflict between F.L.A.G. and Kanshu - and to a mysterious cocoon that would change his life forever, for better or worse…

Hikaru Onuki is a 22 year old girl whose hobby is to cook homemade cuisine in order to find a boyfriend. But for some reason, no matter how hard she tries, she is unable to find one.

High-schooler Shiina Shinya thinks that all girls are pretty much good-for-nothing, mostly because he doesn't understand them at all. That doesn't stop him from being surrounded by strange girls.
Tsubasa Tooka, a cute, much-admired girl, stalks him. Shikimura Masami is majorly into masochism, and has recruited Shinya into her play sessions. Ikari Satsuki seems suspiciously interested in the recent serial stabbings, and seems to want to drag Shinya into it. Banjou Yoruko, a normally quiet, bookish girl, has decided she and Shinya are bound up in some fantasy setting. Uchida Yumeji is the school's sleeping beauty, who spends all of her time in the infirmary because she requires so much sleep. Shinya brings her newspapers, so she can keep up with current events in the short time she spends awake. Lastly, Okui Akane is convinced she is a vampire. For all Shinya knows, it could be true, but in practice it just means that he has to let her drink his blood.
How will Shinya deal with all these good-for-nothing girls that complicate his life?

From: Easy Going Scans

The story begins to unfold in 900-960 AD, later Zhou dynasty, when Chi Wu is being imprisoned after purposely losing to the emperor. His true goal lies within the prison itself, a clue to the whereabouts of world's greatest lost treasure-- Qi Lin Treasure. The words of his capture quickly spread to the ear of his senior and a former officer of the imperial court. Tie Zong Heng (Lawless), decides to be re-enlisted to the imperial services just to hunt down Chi Wu.

Tokano Yuuka has been going out with her boyfriend Yazaki Norikazu for a little over a year now but doesn’t get to see him everyday since he works in a different city as a newspaper reporter. Although they are apart, they love each other and things are going well. Norikazu gets an opportunity to interview Saeki Keito, the lead singer of the most popular band in Japan, Zero Sum Game, because they were good friends in high school. Being a fan of the band, Yuuka gets to tag along. However, Yuuka gets raped by members of the band while Keito distracts Norikazu elsewhere. It seems that Keito is infatuated with Norikazu and wants Yuuka out of the way. After the traumatic event, the relationship between the three becomes extremely complicated.

Akira lives in Ilvia, a town protected by the angels. At the age of fourteen, the children in the sanctuary leave to go to "paradise." However, after sneaking out of the town and meeting a devil, Akira discovers that the angels and his peaceful is not what it seems to be.

A collection of sweet, realistic tales about the everyday lives of various cats and the people who come to associate them.

The world has become a desolate, lawless land where bandits roam free, innocent people suffer, and demons lurk around every corner. Souna Yuuki is traveling with his family when they are attacked by bandits. His entire family is murdered, and he is left with a snake mark on his hand. As he is about to die, a woman comes up to him and gives him an option: continue to live in this harsh environment or die peacefully now. Yuuki chooses life and Garami, the woman, gives him a second chance at life in exchange for his servitude. Garami is a weapons merchant and a gun for hire that travels from town to town for clients. Yuuki sees how brutal and unforgiving this world can truly be.

Long ago, a powerful demon lord ruled over the people until an equally powerful hero rose up to defeat him. To counter future threats, Rosewood Academy, a school for heroes-in-training, was created. Today, Rosewood Academy enrolls only the best of the best, and Arnest Flaming is the best of them all. The top student in the school, a dutiful girl nicknamed "Empress of Flame," she has an irritating encounter with a light-hearted boy in the school hallway one day who seems to equal her powers, though she's never seen him before. He introduces himself only as Blade, and Arnest soon finds out not only is he transferring into the school as a new student, but she is personally requested by the King to help him settle in to daily life in Rosewood Academy.

A compilation of additional tips written by Ryukishi07 outside of the games. Several of the stories are humorous in tone, but the more serious ones may be considered canon.

The story of a highschool girl who seems to get lost quite often, stumbles upon a train station that shouldn't exist, and a restaurant in front of it with very strange clientele. What will become of her after being forced to start working there?

On the very first day that Kuze Aoi transferred to Hinomiya Academy, he finds himself facing down the barrel of a gun. He is introduced to the campus and the student body by his childhood friend Miyabi and learns about the prince and princess among students, Shitara Sagiri and Hinomiya Kuon. Sagiri is a cool and beautiful while Kuon is elegant and magnificent. After school, Aoi gets lost on campus and Kuon begins shooting at him and he's barely saved by a random girl named Atarashi Sonoko. It seems that Aoi holds a secret that is critical in a feud between two old, powerful families.

This beautifully drawn short story by Yôko Nihonbashi, creator of G senjô Heaven’s Door, introduces the silent, beautiful Yaeko Shimura, a woman who brings new meaning to the words dutiful wife and good friend.

Note: The pilot oneshot has been scanlated, but not the compiled volume.

From Etc:
Based on historical setting of Korea during the Josun Age. Long ago, in Jushin, secret royal inspectors named "Angyo Onshi" wandered the country and restored the order. But now that Jushin is destroyed, only one is still wandering.

The continuing adventures of classic Arsene Lupin character created by Maurice Leblanc. The manga adapts Maurice Leblanc's novels about a gentleman thief who solves cases while outwitting both the police and criminals. The first chapter of the manga retells the first short story Leblanc published, "The Arrest of Arsène Lupin" (1905). Lupin is a Gentleman Thief and a master on disguise, during the Belle Époque years.

A collection of 24 short stories about the troubles and stress at work faced by a wide variety of people, including a novelist, a dancer with a secret, a rabbit-powered bus driver and an elephant tamer.

Includes:
She Got Off the Bus at the Peninsula:
Mitsuko Kunizaki has inherited a small grocery store from her grandmother. Being a single mother to a little boy, she intends to close it down and move on with life. However, in the solitary store that sits next to the last bus stop at the tip of a peninsula lie some long-buried memories that slowly reemerge as Mitsuko arrives at what used to be her home—memories of a lonesome childhood and of people who came to the peninsula to end their lives.

The Labyrinth Cat:
Residents who have just moved in are always lost in this complex apartment. However, there is one little feline that will help them get back to their apartment house.

Bio Luminescence (created under the pen-name Soyogo Shima)

Also includes two Mushishi stories set in modern day Japan and with different characters than the long running series.