Based on the visual novel Tomoyo After (a Clannad spin-off), this manga retells the story from Tomoyo's perspective.

From Tokyopop:
An introspective, character-driven series, Tokyo Babylon reads like a manga version of The X-Files. Its story -- a modern-day fantasy -- follows a young onmyouji (spiritual medium) on his quest to protect Tokyo from evil spirits.
Teenaged Subaru Sumeragi is the 13th head of the Sumeragi clan. Together with his twin sister Hokuto and the mysterious veterinarian Seishirou, Subaru travels around Tokyo, calming the ghosts that threaten the city.

A collection of oneshots:

1) Tokyo Ants
A special security group consisting of highly-skilled people rescues a hostage.

2) Enma 1 & 2
Two different stories about people who can see electricity when someone tells a lie. (Enma 2 story by: Ookawara Ton)

3) Butterfly: Swallow Tail
About a boy who can see swallowtail butterflies around people who are going to die.

Short story collection of a variety of more mature Tezuka work. The story "Clockwork Apple" was borrowed from the book, before the movie was made, but has very little to do with the book either as Tezuka admits to writing it without reading Clockwork Orange.

From Operation Boredom:

Jin, son of a Count, has a dark past that follows him everywhere. Now a pirate, he's recently acquired a new set of slaves to sell. However, one of them, Lisa, sparks something inside Jin. Could she be the one to get through his cold, ruthless, and dark heart and see what's really inside him?

The third entry from the infamous God series of web manga. This is what happens when the creator of "Umbrella Sword" tries to make a love comedy.

From iskultrip Scans:
Due to the influence of the "Dragon veins", some young men and women awoke as "those with power". They'll discover their "star of fate" in a struggle to the death with the "oni" attacking Tokyo!!! The super popular action anime has become a fantastic comic!!

From Loyal Kiss:

Guo Guo's father had wished for her to go to college, so when he died, her mother tried to fulfill his dying wish more than ever. As a result, Guo Guo constantly skips school. Lian is the only one who can help her. What will her final answer be?

A collection of shorts by Byungjun Byun, artist of young sensible works on the life in the city, including "Princess Anna" and "Run, Bonggu". Many included shorts have received renowned awards from Korea and Japan.

Hachiouji Tarou is an average 2nd year high school student. Since his father died, leaving him as the head of the family, he’s been constantly pulling his brother out of trouble. One night, when he came back home, his mother's head was rolling on the floor, and an evil spirit had hold of his younger brother. Instead of helping him, he hesitated and stood frozen with fear while the spirit got away with his brother. Now Tarou is on a quest to find his brother and exterminate evil spirits.

A story of three childhood friends - Colo, Cookie, and Naomi - who grew up in a sleepy backwater town on an uncivilized planet. They struggle to get by while holding on to their dreams of leaving town and finding a better life but can their friendship endure the tests of time? Can it withstand invading armies, broken dreams, conflicting ambitions, divided loyalties, jealousy and even betrayal?

Based on the visual novel of the same name. In 1986, between October 4th and 5th, members of the Ushiromiya family gather on the secluded island of Rokkenjima to discuss the division of the family's massive fortune upon the impending death of the family's head, Kinzo. However, when a typhoon traps the eighteen people present on the island, six people are mysteriously murdered. The remaining people struggle to survive as the murders continue, supposedly by the will of the legendary Golden Witch, Beatrice.

Other manga:
+ Triage X manga
+ Sidonia no Kishi manga

From MangaHelpers:
After a terrible earthquake, Satoru wakes up in a pitch black cave that him and his friends were exploring. Desperately moving through the crumbling cave with just his backpack, he expects a warm rescue once he gets out. But what awaits Satoru was an unbelievable fact: Japan has sunk underwater due to the earthquake and he is stranded on an island with no one to help him. Can Satoru learn how to survive by himself?

When a genius manhua artist enters the world created byhis own pen, where humans and fantastical creaturescoexist, he is determined to become the god reigning overthis world. However, things are not as simple as he thinks.Will he become the god of this world, or will he only barelyscrape by to survive?

Summary refers to the Ohzora Shuppan re-print, 2007:

1. Lovers and Souls
Shinomiya is a beautiful college art student who lacks the morals common to most people. After agreeing to be a nude model for Matsuoka, a photography student, he also agrees to sleep with him for money even though he is straight. However, what started as a small taste of the forbidden soon spirals out of control when Shinomiya begins selling his body to other guys as a prostitute in a male brothel. Can Matsuoka save Shinomiya from himself?

2. Vanity
After the events of Lovers and Souls, Tooru is still deeply heartbroken. Trying to find solace in Hikaru, Tooru challenges the terms of their friendship. But can he handle the consequences?

3. Sleeping Beauty
Matsuoka sees Tooru for the first time.

4. A Moon in Name Only
In their last year of high school, Akihiko Nozaki admits to his best friend Kai that he's gay. Kai is stunned but it doesn't change their friendship, but Kai's curiosity is aroused and he begins to see Nozaki differently.

5. The Name of that Sky
Sequel to "A Moon in Name Only", told more from Nozaki's point of view. Nozaki isn't sure whether to trust that his relationship with Kai will last, since he's even been dumped by gay men before. What's to keep a guy who wasn't even gay from breaking up with him?

Part of Rules / Hydra Series

From Storm in Heaven: Koizumi Kanna is infatuated with the man who came to the restaurant she works at and ordered a burger with no onions. Little does she know, Toujou Ren is interested in her as well, but for a different reason. Kanna just so happens to be the mirror image of a woman he knew a very long time ago. It is for that reason that he saves her when she nearly dies in a car accident. But the life he gives Kanna is far different from the one she lived before, and she's not certain it's the kind she wants...

From Valkyrie Scanlations:

The princess of the kingdom of Dipan, Alicia, was abandoned by her parents when she was still a child. The rumour says that she was posessed by a Demon and therefore lost her life. But the truth reveals different. Alicia in truth, inherits the soul of the Battle Maiden Silmeria, one of the three Valkyries, what she has to hide from the rest of the world. That of course gives people reason to think she has a split personality. She is taken to a castle far away from her kingdom and hidden from the public and ever since living a quiet life. Until that one day when Odin, the lord of the gods, decides to come after the lost Valkyrie and forces her to return to Valhalla...

1-4) Beautiful, Beautiful, Beautiful
After the break-up with his girlfriend, Kou is left very upset, which is when he meets Akio, Mai's brother. The two of them don't exactly hit it off, but there's a strange kind of attraction that keeps drawing them together.

5) White Fingered Demon
Junior is the son of an Irish mob boss in 1930's America. His father's lieutenant, Leonard Lang is like an older brother to him, but as Junior gets older his feelings for Leo are beginning to change.

Two kids become friends, even though he has an incurable illness. One winter, he was told he wouldn't be able to live to the next spring and she...

Collection of oneshots:

1) Saigo ni, Kimi Dake wo
Hero has been inseparably bound up with his selfish friend from his childhood. He is called and comforts him whenever his friend parts from his lovers. His friend confesses his love to hero only after they fall over the cliff and is going to die...

2) Love Letter
An urban delinquent student is transferred to a local school by his parents' order. There he is stalked by a rude but pure local student...

3) My Most Beloved One Is Still You
A supervisor and his subordinate love each other. Returning from business tour of 3 months, the beautiful subordinate has become fat...

4) Koi no Sokubaku
A new recruit keeps working overtime with his wish to be admired by his supervisor. But his colleague puts the blame on him. The supervisor gets him mixed up with an industrial spy and tortures him...

5) Late Night Rain
Many people have tried to persuade a surgeon of genius to reactivate in vain. The surgeon keeps living in seclusion because he failed the operation of his lover's brain cancer and has a lapse of confidence. One boy starts working as his live-in housekeeper but the boy is his ex-patient of the surgeon and doesn't have much time...

6) A Liar
A boy loves his pet, an android. But the android returns sweet nothings to the boy because the android has no feeling. A fire occurs. The android takes his life upon saving the boy. Decrypting the microchip of the android in the cold ashes, plenty words of love are displayed on the full screen...