From The Zero Alliance:

A young girl called Ene is searching for her parents? killer, Estoma. Her search leads her to a strange gravedigger called Mal, who she works with to find out a way to kill the immortal Estoma.

From Lililicious:

Madoka tells Mayu she likes her and then runs away when Mayu asks her out. Mayu tracks her down and the two of them begin dating, but there's something Madoka isn't telling her...

Lily Liemola is a powerful swordsman with rather old-fashioned ideals about honourable battle. When he hears of a "legendary fighter" named Albert Wilhelmus who many skilled combatants have failed to even approach - let alone defeat - Liemola wastes no time in challenging this man to a duel.

A collection of stories:

• Priceless Honey (chap 1-2)
Suguri Nagisa, the custodian at an all-boys' school, works at a secret - and quite risque - part-time job. But what happens when a teacher from the school discovers "Call Boy" Nagisa?

• Fine Play
Nanafuji is a regular customer at the cafe where Kaji works at as a waiter. The two became quite friendly when Kaji returned Nanafuji's lost cellphone to him. Kaji told Nanafuji that he had a problem with a stalker and the latter suggested that he should pretend to be Kaji's lover to make the stalker give up on Kaji...

• Yandere Master

• Replay
At his brother's wedding, Fumiya sees Mitsugu for the first time in six years. With their complicated history, and Mitsugu's feelings for Fumiya's brother, they have a lot to hash out.

• Fall in XXX
Both wear glasses, but their personalities are too different. Tadashi's senpai is studying hard to get into Tokyo University to chase after a girl, so they have become classmates at prep school. One night, his senpai invites Tadashi over to help study for the secondary exams. What will Tadashi do with the feelings that he's kept hidden for so long, let they're alone in his senpai's room...

• Back Stage
Sequel to chap 3

From Yes_Rhade:

Kaname and Tooru have been lovers for three years, but Kaname just can't accept their love. Why? Kaname is Tooru's uncle, and no matter how much Kaname loves Tooru, he realizes that their relationship is wrong and should not continue.

"Original" doujinshi by the circle Sanninda-Kikaku.

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?