From the Animeraider:

Have you ever read a manga and thought to yourself, "Why the hell did he do that? It's not what I would have done. I could do better!" Well, now here's your chance. This manga changes storyline depending upon choices you, the reader, make. Have fun!

"Do Your Best, Chrono-kun!" is a short manga that was included with the Japanese game guide. In full-color glory, this manga recreates the beginning of the game, where Chrono meets Marle during the Millenium Fair. The art style is a fair imitation of Akira Toriyama's, a plus for those who are so inclined.

In the Docchi mo Docchi series:

V.1 - どっちもどっち Docchi mo Docchi
From their offices high up in a corporate skyscraper, alpha males Ozaki and Tsuburaya make all the ladies swoon. Ozaki's known for his irresistible pheromones, while Tsuburaya's a noble, worldly genius. But when these two rivals end up in bed together, who will come out on top? It's seme versus seme...and much more than pride's on the line!

V.2 - どっちもどっち! ! Docchi mo Docchi!!
At long last, the battle to become top dog - literally - produces a clear victor. But who will it be?

V.3 - どっちもどっち! ! ! ~第三のイケメン~ Docchi mo Docchi!!! - Daisan no Ikemen

V.4 - どっちもどっち！！！～厄介なイケメン～ Docchi mo Docchi!!! - Yakkai na Ikemen

V.5 - どっちもどっち! ! ! ~覚悟のプロポーズ~ Docchi mo docchi!!! - Kakugo no Propose

V.6 - どっちもどっち! ! ! ~ないしょの遊び~ Docchi mo docchi!!! - Naisho no Asobi

Nonaga Hiromasa is an up and coming soccer coach who has made a name for himself for bringing multiple teams from literally nothing to the top in the country. What’s even more impressive is that he just entered high school! He was recruited into his current high school as the new soccer coach, and his observation skills and ability to predict the opponents’ movement make his sole presence enough to win games.

The fact that Hiromasa is going to be coaching at the high school has many top soccer players flocking to this school, but none stand out more to him than Sakamichi Kappo. Not only can Kappo score a goal from half field with his powerful kick, but his ball control is second to none. Initially, Kappo didn’t want to play on a team because he thought no one understood “his soccer style,” but when Hiromasa was able to understand it, Kappo decideds to play for the team. Will the brilliant coach and the talented player be able to take the high school soccer world by storm?

In the Doctor's Rule series:

* Vol 1 - Doctor's Rule

• Nakajima is called for backup at the hospital Kurata is working. When they were high school students, Kurata and Nakajima were lovers but Nakajima unilaterally forced a rule on Kurata to not have eye contact with him and he finally ran away from Kurata. On the other hand Nakajima realizes that his disquiet never disappears...

• 2 students of an acting school are working part-time in Kurata's hospital. One aims at getting a wealthy man and Kurata gives him a ticket for a mixer where adult guys who like young boys will gather...

• Because of their battle of ego, rival attorneys play a game where the loser must be a slave...

• Angst between an elite career inspector and a detective under his jurisdiction.

* Vol 2 - Amai Kusuri

Contains two stories:

Chapters 1-3 -- Dokusaisha Granada
Naruse Kunihiko is an upcoming short film-maker who shares the spotlight with no one. He writes his own scripts, his own music, and uses the one-man art of claymation to realize his vision onscreen. An arrogant artist who doesn't tolerate any criticism, he operates solely on the desire for praise. So when he forms a friendship with Nakata, a journalist who has been assigned to interview him, Naruse finds himself unprepared for the trials of a real human relationship...

Chapters 4-5 -- Birthday

Two students, one popular and the other an antisocial loner seemingly unconnected except by the window's reflection but looking past the surface perhaps they have more in common than either thought.

1. Hen Koi no Specialist

2. Oyasumi Manatsu no Gatsu

3. Koi no Jitsuryoku Ai no Sainou

4. Dokusen Happiness
All Sonoko wants for Christmas is to spend it with her boyfriend. However, it seems that he can’t spare her a few minutes on Christmas, as she’s not his top priority. To make things worse, she’s starting to feel more and more drawn to Takatsuki, a classmate who once confessed his feelings to her…

From Evil Flowers:

How many doors must you open before you can reach heaven? Is it after the next one, or the one after the next one?

In a school where after school activities are mandatory among all students, Hajime and her friend Sayo come across a new club that they have never seen before. The club is called "The Cultural Activity Preservation Club." The two enter the room to find all kinds of analog jobs and activities, such as handcrafting mats and toothpicks. This is a unique cultural manga mixed with comedy so as not to bore you, this is Double J!

A touching story of a doctor who wanted to help people even though he became a vampire.

In an future apocalyptic world the church once again has regained power, but not to do good, but to serve evil. Cloned priests, called "dragon fly" of the kirihito church use their power, however a shinigami has appeared to stop them and reclaim her past...

The story follows Erina's route in the Dracu-Riot game. Erina is a foreign vampire from Russia and she is very ecchi, her conversations often involve ecchi stuff which makes Azusa really edgy and Yuuto nervous.

A collection of Dragon Kishidan oneshots and side stories:

One Day, Another Day
Set before the end of the series, it's basically a side story of a day in the Dragon Castle, kind of in Zoma's perspective.

Juuji ni Hikaru Hoshi
Takes place before the events of the actual series. This is a back story that shows how Lykouleon and Raselane met, introducing Lykouleon's uncle, Fieruto.

Mamono no Mori no Kioku
Another backstory that delves a little bit more into the relationship between Bierrez and Cesia before the series started. It also shows how Nadil became the demon lord.

Happiest Children
This actually has three little side stories in it. The first one is about Rune's dream about everyone dressed in drag, the second is about a little adventure that the three dragons go on, and then the third is like a day in the life of Alfeegi, Ri-ma, and Duma.

Crescendo
Backstory about how Lykouleon and Kaistern met and how Kaistern then became the Blue Dragon Officer.

CONFESSION - Thats
This is basically the backstory of Thatz and how he knew about Rath's little secret.

CONFESSION - Rath
Basically telling a lot about Rath, particularly his relationship with Kaister.

A collection of mildly ecchi otokonoko-styled stories focusing on crossdressing high-school boys and the boys who like them, mostly from the men's magazine Oto Nyan. Some of the stories are continued in Hiriajuu Shuudan ga Classmate o Josousasete Kanojo ni Shite Mita.

1-3. Raising Decoy
A boy helps his classmate go undercover in drag to catch subway gropers, and finds that he looks disturbingly good in a dress....

4. Ato no Matsuri (retitled Spilled Milk in the English edition)
A group of male students, having failed to get girlfriends, are becoming desperate; what will these "innocent" boys resort to?

5. Tenshi no Houbutsusen (Parabola)
Baseball-themed romance short.

6. Actress
A boy joins his high school's film club to meet the actress from their amateur film, but gets a surprise...

7. Shishiza no Boku to Natsu no Yozora (retitled Leo and the Night Sky of Summer in the English edition)
The president of the school astronomy club wants to catch UFOs.. maybe some "sexy female alien" costumes will help?

Based on Massively Multiplayer Online Game (MMOG). The beautiful Goddess Altea, creator of the tranquil worlds of Lagendia, plummeted into unconsciousness after being poisoned by her jealous, evil sister Vestinel. The poison can only be neutralized by an antidote made from the source of the poison itself - Vestinel's magic grail - which has disappeared into Lagendia along with sinister Vestinel herself. Able to communicate to her people only through dreams, the Goddess Altea calls upon the Heroes of Lagendia, via all-knowing prophets, to find the grail and save her from her eternal slumber. In their quest, the bold warriors must comb the lands for enchanged Power Stones, which allow them to speak with the prophets and unlock the will of Altea through her dreams. But the hunt for the Power Stones is not for the meek, as since the Goddess Altea's poisoning, the formerly peaceful lands of Lagendia have become home to throngs of deadly dragons bent on thwarting the grail's discovery and keeping the land in despair.

From Iskultrip Scans:

In order to restore the Great Dream Tree of Elfland to life, Kiki, a mare, has to eat bad dreams that plague people’s hearts and foster good dreams so that they sleep well. Aided by Gilly, the tree guardian, and the garden elves, she wanders the human world. However, the world is a dangerous place...

Volume 1: Dream Eater
Volume 2: Dream Eater - Saigo no Yume

This story acts as a sequel to the original "Dragon Quest Monsters" game for the Gameboy. Kurio, a child who wishes to be a hero, is thrown to a world where monsters are found all over, and is asked to become their new Monster Master hero since the great tree is withering, the monsters are going berserk, and Terry, the previous monster master, has gone missing.

The year is 2029, and Hibino is an ex-police officer who now makes a living running errands for the leader of what appears to be a high-end gang. But how do a civil uprising in Niger, the attack on a radical military figure in Japan, and a bone-marrow thief tastelessly dubbed "The Vampire" connect Hibino to the mysterious white-haired boy who is forever confined to an enormous library reading through scores of books?

From Sugar Oasis:

Riria is a middle school girl who is absolutely, hopelessly in love with the guy who lives next door. The only problem is that he is a LOT older than her. His name is Rinpei, and he is 26 and a businessman from a rich family. Although he is nice to Riria, he (rightfully) considers her just a kid, and just treats her like a friend. Poor Riria, she loves Rinpei so much, but he is so much older and doesn't see her as a real woman.
To solve the age problem, Riria transforms herself into a totally different person, trying to make herself look older. Now is the test, she decided to find Rinpei on the street and see if she can fool him with her 'disguise' into considering her a real 'woman' and see how he likes her then. Amazingly enough, things go well. Riria, in her new persona manages to make quite an impression on Rinpei! In fact, he really likes her!