This is Masashi Kishimoto's manga, Karakuri. It was created before Naruto and was collected in Naruto: The Official Premium Fanbook.

In order to combat a deadly virus, an implant was made that is transplanted into a human being's nervous system. Unfortunately, this implant technology was also used by the less scrupulous to create human weapons, blood-red eyed creatures referred to as "Roido". To cope with this threat the defense agency has created the Karakuri unit, an elite unit whose human members are monitored by small talking animals. As Kiru the karakuri goes to visit his friends Koten and Koron while on leave, he's going to learn that there are no days off against the Roido!

Kagura is a professional slacker with nothing but a part-time job and cram school to keep him company. When a little girl suddenly shows up in his house one day, he thinks things can't get any weirder... until she starts calling him "Daddy"! It's hard enough taking care of an ordinary child, but Kanna -- who doesn't speak his language, isn't from his dimension, and has hordes of evil minions hot on her heels -- is anything but ordinary!

Girard and ViVi are special government agents known as "Right Arms" whose job is to seek and destroy people who have become infected.

In their world, a weird virus that turns people into monsters has run rampant. The only way humanity can survive is to keep tight control on the infected to prevent the spread of the virus. If the virus' symptoms appear, the person must be disposed of. It's a tough world where even children must sometimes be killed to give humanity as a whole a chance to survive.

Tetsunosuke Yamabuki enrolls in the police to follow in his fathers footsteps. Some events lead him to discover that his father might have had links with a secret branch called the death brigade, and he is led to enter it himself. Wacky adventures and hilarity ensues.

Goemon Ishikawa, the legendary king of thieves from the feudal era, has come to know that there is an important treasure being transported from the Imperial Palace to the Kamiyama mansion; an ancient artifact called "moon's melody box" (月詠みの箱). Surprised by the extreme measures taken by the guards of this treasure, his indomitable spirit aches to steal this rare item that once a year can grant one special wish to whoever possesses the box, but it will not be so easy to steal it. Even worse, once it is opened, it will be harder to deal with the unusual contents of the box.

Karugasaki Tora decided to repeat a grade and turn into a delinquent just so he could be popular, on his best friends advice. However, his plan backfired and nobody talks to him in his new classroom. The only thing he can look forward to is seeing the cute girl sitting next to him, but after trying to talk to her she immediately kicked him and threw him out the window. Later the same day, though, he saved her and a little girl from being hit by a truck. No longer able to avoid him, the girl reveals that she's a ghost playing a shinigami's game. She must get the boy she likes to return her feelings at times given by a pair of hourglasses so she can return to life, or fail and be sent to hell together. Unfortunately, her feelings have awakened for Karugasaki...

From Mobots:
Rumina Asagi is high school student, who dreams of a 'rose-colored life' with a cute girl. Along with his science otaku friend, Ginnosuke Isuzu, he lives a pretty normal life. Until the day that he discovers a huge hole in his backyard, along with two women, one a hot tempered blonde (Chelsea Rorec) and the other... the girl of his dreams (Ruri Sarasa). But... where did that hole come from?

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In the year UC 0079, during the One Year War of the first Gundam series and eight years before the story in Zeta Gundam, a boy named Van Asiliaino and his friends attempt to flee the war, and their fates change when they meet a certain soldier.

Set in Universal Century 0092, the Earth Federation has a tactical advantage over Neo Zeon forces stationed on Earth. Despite this, a few Earth-based units have decided to make their way back to space while some would stay behind and conduct guerrilla warfare against them. It is about a Federation attack on a Zeon base in Scandinavia involving pilot Frederick F. Brown.

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To celebrate the upcoming live action movie, Nobuhiro Watsuki reinvents the classic Rurouni Kenshin manga with all-new twists and turns.

Action, romance, and historical intrigue abound in Rurouni Kenshin, the tale of a wandering swordsman during Japan's chaotic Meiji Restoration. Join Kenshin, Kaoru, Yahiko, and others as they take up their swords once again!

From Bakaupdates: Leopold Fieseler, a detective with the Zeon Public Peace Department/Zeon Public Safety Department is charged with investigating terrorist attacks against Zeon government officials led by an anti-Zabi group called Valkyrie. While researching to find out who were the culprits, Leopold gets into trouble when Valkryie supporters within the ZPPD/ZPSD "arrest" him for getting his hands into classified information to help find out who are the culprits for a planned terrorist attack against Gihren Zabi himself.

A direct sequel to Mobile Suit Gundam, and a prequel to Gundam 0083 and Zeta/ZZ Gundam, CDA tells the story of Colonel Char Aznable directly after the One Year War. He heads toward Axis after the battle of A Baoa Qu with the remaining Zeon forces, where he meets a 14-year old Haman Karn, who begins to fall in love with Char. Char must also deal with Colonel Enzo, who plans to restart the war with the EFSF.

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A family drama which goes over three generations. From the Battle of Jaburo in U.C 0079 to the battle with the Crosbone Vanguard in U.C 0123. Kamuna Tachibana who grows from a green 21 year old ensign to the 65 year old Veteran commander of the frontier side. In the middle of fighting the Vanguard, he notices that the commander of the enemy MS forces is none other than his son Syun. Wondering where he made a mistake, Kamuna looks back to the past and tries to find an answer

"Justice is within your heart!"
Welcome to the Misaki Academy, a futuristic island-sized school where students' freedom is valued above all else. This lack of restrictions has lead to the founding of some very unusual extracurricular activities and groups, like the World Domination Club. When the World Domination Club attempt to control the school lunch program, cute high school girl Hayana Suzunari decides to take a stand, becoming Twinkle Saber, defender of justice!
The series that took the amateur press manga industry by storm is now widely available as "Twinkle Saber NOVA"!

Alternative Summary:
Hayana and Aoi go to Misaki Academy, where their favorite pastime is to eat at all the local restaurants. Misaki is known for it's lax importance on rules, and while that means freedom, it can mean trouble. Hayana's lunch gets interrupted one day by a new club... the World Domination Club! (They're starting with the school lunch program and working outwards.) Luckily, Hayana gets some help from one of her teachers and joins the Ally of Justice Club as Twinkle Saber, sworn to defend the lunchtime (and truth and justice along the way) of Misaki Academy against the World Domination Club!

From Studio ADTRW: After suffering numerous interstellar wars, mankind has finally formed an interstellar union. However there are still many disputes and wars occurring amongst the members of the union itself. In order to resolve these problems, a secret organization, known as GOTT, is formed. They employ agents with special powers to fight for the organization. Agents Eclair and Lumiere are two girls with outstanding abilities, and they are assigned as partners. Together, they fight, and slowly uncover more and more about the secret of the organization that they work for. Note: Dragon Jr version, less serious and more chibi-looking than the Shounen Ace version