The locomotive called the Rainbow Stone Train runs, not on electricity, but on the energy source called, "Rainbow Stone." Inside, the train is split; from the extremely high class Evening carriage, to the average Afternoon carriage, and finally, to the cheap, but cramped and noisy, Morning carriage.
Employed as a crew member of Morning, Toky Towy struggles daily by the side of his strict superior. While going through various encounters and farewells again and again, he...

To learn about his roots, Sharaku must investigate the mysterious ruins that a long-lost civilization called the Three-Eyed Ones bequeathed to him. In his worldwide search, which takes both him and Chiyoko Wato to locations like Arizona, Easter Island, and Mexico, Sharaku deciphers ancient scriptures and uses gadgets he invents to help solve (or start) problems and mysteries.

Sharaku is frequently bullied for his childishness, and as such the story is also about how he fights back when the x-shaped bandage that covers his third eye is removed. Behind the bandage is hidden Sharaku's malicious third eye, and the boy's hidden evil genius emerges when it can see. Sharaku's rivalries with teachers or students are occasionally developed into major plot points.

Winner of the 1st Kondansha Manga Awards (1977) in the shounen category (tied with Black Jack).

From DrCoke at MangaHelpers:
Set in the fantasy world of Material Puzzle, a manga done by the same author, Berji, Shuga, and Chrim live peacefully on a sparsely populated island. Berji and Shuga have unique talents that allow them to tame animals called Deathleon. On one peaceful day, an uninvited large ship arrives at their island. The ship belongs to the "Ironclad Giant" Suppression Team, and with them, they brought a piece of an Ironclad Giant. What this ship and its crew brings to the inhabitants of the island may change the world forever.

A boy goes looking for the legendary magicians who can save his village from a giant fungus, but he finds more than he bargained for.

A girl is saved by a fox and goes on an extraordinary adventure.

In a world that has become 70% harsh desert, the Rainbow Council of the International Peace Keeping Forces, a team of super-powered global security guardians, have a growing crisis on their hands. No. 5, one of their own and known within the council as their top marksman, has left his post and gone rogue. It's up to the other guardians to track him down--but No. 5, with his mysterious companion Matroshka, won't go down without a fight.

From: Easy Going Scans

The country of Greenland, after losing the war to the Imperial Army, were in agony and despair for what will the future bring them. They had hired mercenaries to help them during the war and now they've come back to collect their reward while the country were still picking up their pieces of their broken dreams. By that time, the King has passed away and his heir was still too young to take up on the throne. After hearing the news of the King's death the mercenaries decided to take over the throne and rule in his place. But there was an obstacle in their way... The Oracle!

In the story, for generations the men of the Susuhara family have, upon reaching a certain age, left home and gone their own way, living alone with no one to depend on until they are acknowledged. The protagonist is a high school student who has left home and is comfortable at his new school. But there's a strange girl named Toe Kurokami. She carries what appears to be Japanese doll, and he's sure its hair grows and it whispers things. Meeting her might be his destiny.

Follow Sudi, the traveling performer and Blackie, the talking cat through time as they try and find the mythic Angel Tear and make some cash along the way. A three arc story about angels, love, betrayal and beautiful men!

Set in an alternate 1940s, Jackie Rose is a rip-roaring adventure story filled with excitement and fun, that still manages to tug at the heart strings.

Original Webtoon

A thousand years before Christ, the last king of an ancient dynasty was seduced by a fox spirit that caused chaos in his land and drove his people to despair, before she killed the king and was finally sealed by an exorcist. During the Heian Period that golden-haired, nine-tailed vixen, known as Daji in China and Kayo in India, reappeared in Japan...

In Kyoto, misfortune befalls Mikuzu's family after her father nearly shoots a fox with an arrow. Now Mikuzu, with the help of her neighbour and a childhood friend Oniomaru, is looking for a way to cure him. But once the fox spirit abducts Mikuzu, meaning to recommence her misadventures in a new incarnation, the battle to save the girl and to restore the seal begins.

The prince, His Majesty Viloftira, begins a journey, seeking the sword which will allow him to succeed the current king. The one who will accompany the Prince on his dangerous journey through this fairy tale land is Pierre, his new and unfortunate attendant.

Sable Prince is a travel fantasy story, intertwined with the relationship between a (lazy) tyrannical prince and his new mysterious attendant.

Two soldiers from warring countries are bound by a pledge as master and servant. Taki Reizen is a commander of sublime beauty, shouldering the fate of his nation. Called "Mad Dog" because of his rough temperament, Klaus von Wolfstadt has sworn his loyalty to him as a knight. Despite this, those around them are cold and disapproving, full of various misgivings. For all their genuine feelings, what will come of love made cruel by the violence of war?

A thousand years before Christ, the last king of an ancient dynasty had to sacrifice his own life and that of his friends and allies to seal away a demon fox causing chaos in his land and driving people to despair. During the Heian period that golden-haired nine-tailed vixen, known as Daji in China and Kayo in India, whose malign influence led to the dramatic downfall of the governments, reappeared in Japan...In Kyoto, a misfortune befalls Mikuzu's family after the head of the household nearly shoots a fox with an arrow. Now Mikuzu, a daughter of a ronin, with a help of her neighbour and a childhood friend Onioumaru, is looking for a way to cure her gravely ill father. Once the demon fox abducts Mikuzu, meaning to recommence her misadventures in a new incarnation, the battle to save the girl and to restore the seal begins.

A trans-dimensional fantasy.

A young boy's curiosity leads him to attempt an urban myth which sends him to a dimension called 'The White World'. There he meets a young man who sends him to a world called 'Devildom', he ends up landing in water in a kingdom called 'Kyungma' and nearly drowns until he is saved by a mysterious young girl who seems to control water...

The curse of twelve stars, a girl who plays piano with a dream of becoming a chef, because of an odd job that she pretends to be a boy. What's waiting for Yue Hui is a mysterious mansion and 12 boys who have the curse of 12 stars which fall upon each of them. What's awaiting her? Where are her and the boys' destiny leading to? A love song for 1000 years, the legend of 12 beautiful stars, everything is in《Starry Night Club》

Ciel is a member of the 'fairy-wing conservation group' - an organization that protects fairies from hunters who try to hunt them for their wings, which are said to bring the possessor eternal happiness. Ren is a precocious but immature fairy-wing hunter with a tormented past and a grudge to satiate. The encounter between these two will open the doors to a tale interwoven with fate.