From Tokyopop:
On a world with no women, the surviving men have reintroduced the female in the form of an android. Called Marionettes, they are built to serve men and are limited in their interactions with humans. That is until a poor boy named Otaru Mamiya encounters a Marionette named Lime. Lime is a Saber model with a special circuit that gives her emotions. When Otaru awakens two more Saber Marionettes, his life as an 'average' man quickly becomes as extraordinary as the lives of his eager, busty new friends.

22 years ago a mysterious seismic phenomenon rocked the Yokohama district, thrusting it miles into the sky and effectively separating it from the rest of Japan. In the following years, a fraction of the newborns in this fledgling world began to develop extraordinary powers, each unique to the personality of the possessor. These mutated humans became known as Alters and were responsible for turning the former Yokohama into a chaotic wasteland. Now, as the former metropolis continues to re-build itself, the Alters have fallen into two camps: those who have joined HOLY, a dogmatic organization that hopes to re-establish order and morality, and those who wish to lord over the comparatively weaker humans. Only Kazuma, a powerful Alter who's really only interested in looking out for himself and an orphan girl named Kanami, stands between them, suspicious of both sides and unaware that he may hold the key to harmonious co-existence.

Classic short stories from Takahashi Rumiko. Many are comedies.

Volume 1:
"Fire Tripper" (fantasy, romance)
A gas explosion sends high school girl Suzuko and toddler Shuu 500 years into the past. But she lost Shuu on the way, and as a result, Shuu ended up in the past 10 years before her, and is 15 years old when Suzuko arrives.
"Maris the Chojo" (comedy, sci-fi)
A destructive alien policewoman sees a kidnapped quadrillionaire as her ticket out of debt.
"Those Selfish Aliens" (comedy, fantasy)
Aliens, the government, and fishmen implant bombs in a poor paperboy.
"Time Warp Trouble" (fantasy)
Warriors from feudal Japan inexplicably pop into a high-school classroom.
"The Laughing Target" (drama, romance, supernatural, tragedy)
When they were children, Yuzuru Shiga and his cousin Azusa Shiga were engaged. Azusa aims to make sure that Yuzuru stays hers, no matter what, but Azusa also has a dark secret...

Volume 2:
"Wasted Minds (Dust Spot)" (adventure, comedy, fantasy)
Follows a pair of two bickering government agents, both of whom have special abilities. (A five-part mini-series)
"The Golden Gods of Poverty" (gag comedy)
An unfortunate boy's scientist parents try to use him to make money, but they only succeed in contacting the Seven Lucky Gods, who happen to also be broke.
"The Entrepreneurial Spirit"
A woman leads seminars for a get-rich quick scheme.

Volume 3:
"That Darn Cat" (slice of life)
Takahashi Rumiko remembers having to take care of her neighbor's cat.
"When My Eyes Got Wings"
A couple befriend a sickly child with a secret and his destructive pet bird.
"Wedded Bliss" (comedy, romance)
A wedded couple can only let out their tension from working all day by fighting with one another, until their neighbors threaten to have them moved.
"Sleep and Forget"
A girl relives a past life involving her lover and an evil witch back from the dead in the form of a dog.
"A Cry for Help"
A fairy gives a boy a frightening split personality thanks to the wind-up key she inserts in his neck.
"War Council"
Student councils go to war with one another over a stamp.
"The Face Pack"
A man can change his appearance at will and leads a "masters of disguise" club.

more info here.

1-2) Sensei to Himitsu
Kaji's woken up from his nap hearing popular Tsunoda-sensei getting hot and heavy with another guy! But it's his partner, the plain Aritou-sensei that Kaji can't stop thinking about. Kaji's eyes are being opened as he finds that the needs and dark desires that can bind together lovers aren't always about love...

3-6) Hold me for all of Time
A researcher, Sawatari Kaoru, runs off after finding out that there will be no more funding for his research. As he wanders around he sees an abandoned warehouse where he could use to continue his research with his remaining savings. As he walks inside the building, he meets an arrogant little boy. Surprise ensues as to the boys identity, and the unexpected result of his own research...

Extra) And then...
Continuation of ch.1-2, a little into their future.

On the once-peaceful planet of Industria, constant battles have been fought over control of the planet. Astro is a dim witted but kind boy who tirelessly works to feed his "family," a group of orphaned children. One day, after being fired from his most recent job, the prince of Industria, Bulge, appears in front of him. And even more shocking, Prince Bulge looks and sounds exactly like Astro! One thing leads to another, and Astro now has to take Bulge's place as the heir to the throne of Industria! Suddenly, he's faced with the task of bringing peace and harmony back to this war-torn planet!

- Red Hawk NEO

(From Tranquil Spring) A comedy version of Simoun.

Collection of oneshots:

1) Shiro Neko (The Cat Shiro)
Sensei is a veterinarian who works hard and always sleep in the last train. One day, a boy wake him up and all that he thinks is "Kind childen really do exist"... But is that little kid really kind? Or is he like a stray cat?

2) Sweet Days
Asai and Yoh were childhood friends, but Asai had to move out, so he leaves a lesson to Yoh: "You should get stronger". Years later, Asai is a new student and, whoa, Yoh studies there too, but... He became a deliquent?!

3) And Sheep
"It's impossible to talk to animals", that what Lin said when he was visiting Kuranosuke, a genius that knows everything about quantum physics, fundamental chemistry and medicine. After eating with him, Lin goes home and sleeps. On the next he wake up a little... Animal?!

4) Himitsu no Hanashi (What We Keep Silent About)
Yori has a homossexual brother and he just can't stand that. But, to be more complicated, Kawamori, a close friend, likes him. Yori tries to ignore it, but when a girl appears, what will he do? "What if Kawamori falls for someone else...".

5) Endless End
One day, Akutsu meets Mizumoto in a empty street. "I'm glad I meet you. I was wondering what do to if I were the only one alive". Those meetings keep on going when they are alone, but in school Mizumoto ignores him. Will they only talk in a empty world?

6) Summer Vocation
A extra from Sweet Days, with Asai and Yoh's young brother.

Tenchi Masaki is a shy high school boy, yet honest and hard working. He looks forward to living a basic humble life, taking over his grandfather's shrine. However, nothing is ever as simple as one would want, as Tenchi soon learns. A series of events beginning with the sudden appearance of Ryoko, the space pirate, creates madness in his home. Now he must figure out how to juggle 2 princess's, a space pirate, 2 galaxy police, the worlds most intelligent genius and a Rabbit-turned-Spaceship in his quiet country home.

Heero attempts to live a normal life after the war. But his "peaceful" life is disturbed when someone manages to steal Wing ZERO. He rushes to search for it, and is then faced with an unlikely foe. On all accounts, Ground Zero can be considered a doujinshi due to its lack of consistency and subjected humor. However, it tackles deeply into the characters' morale and philosophies regarding war, peace, and of course, the gundams. Like Battlefield of Pacifists and Blind Target, Ground Zero are *possible* events that take place in between the TV series and the OVA, Endless Waltz.

From Manga Art:
After Daa! Daa! Daa!, Ruu is now a cheerful youth living in his home, Planet Otto. Then, a confused girl named Miu arrives through a wormhole from Earth. Ruu joins up with her and promises to take her home. Unknown to Ruu, Miu is the daughter of the same people who took good care of him in his stay on Earth.

From Viz: The trouble and fun began when ordinary teenager Tenchi Masaki inadvertently released the legendary demon Ryoko from his grandfather's shrine. Turned out Ryoko was actually a marooned space pirate! Since then, she's become Tenchi's unwanted houseguest, attracting a host of other troublemaking alien women: Ayeka, a haughty alien pricess; Sasami, her mischievous little sister; and Washu, Ryoko's mad-scientist "mother." Add Ryo-oh-Ki, an adorable little carrot-eating spaceship, and you've got one full Shinto shrine!

1. Teirui Makura
Popular honor student little brother, Yuua, and his kind older brother, Seigo. One step ahead in the puberty department, Seigo tries to put a little distance between him and his cute little brother. However, the innocent little brother is to blame with his defenseless skinship. Finally, Seigo's lust consumes him and he can't endure anymore. Once Yuua accepted that idea, his desire to be attached to his brother grew stronger every day.

2-3. Finger Biting, The Moon's Colorful Person

4. Choroize! Jigoku
A constant failure at job interviews thanks to his scary expression, Danda's employment agent sends him on a rather unusual assignment.

5. Loup-Garou Gokou extra
A short extra to Loup-Garou Gokou, chapter 9 in Hide and Seek.

6. Natsu ni Shini Yuku Monogatari (Dangerous Symphony)
Rock and Homero live in a world, where all kinds of laws restrict people and you can get arrested for the simplest things. Naturally, being love with another man is frowned upon.

The planet of Salami is almost identical to planet Earth. Judging from the appearance, there's nothing different from Earth... Except... The sense of beauty is VERY different. Aimi is an orphan living with her step-mother and step-sisters, and she is what we consider as being beautiful, but what THEY consider as ugly. Yet, that doesn't end the story. Just by an accident, Aimi somehow stumbles upon Earth and meets Kyou Naruse, a self-centered person, a full-blown "narcissist. Kyou comes in, smooth and suave like any prince should, to help Aimi off her feet but she calls him "ugly!" Our very own Cinderella Story... or not.

This is the story of a boy who one day walks into some strange wood and is saved by a nymphomaniac godess who can not only take over his body (turning it into hers in the process) but can also transform him into a girl.

Sakata Gintoki is a samurai living in an era when samurai are no longer needed.
To add to his troubles, oppressive aliens have moved in to invade. Gintoki lives with Kagura and Shinpachi, taking on odd jobs to make the world a better place... and to pay their rent.

Volume 24 contains Bankara (ばんから)
Volume 38 contains 13 (サーティーン)

In the story it is revealed that when Ichigo Momomiya, the protagonist from the original Tokyo Mew Mew, is studying in England with Masaya Aoyama, Berry Shirayuki is introduced. Berry is trying to adjust to the private school which she has just transferred to. She later runs into Ryou Shirogane, who she follows into Café Mew Mew. While Berry is staring in awe at the cakes and pastries, Ryou sees her and yells, wondering who she is. Berry, caught by surprise, falls on top of the snacks. Embarrassed, she runs with her eyes closed into the employee's only section of the Café, and runs into the DNA-infusion device. She is transformed into a Mew Mew, with the DNA of a rabbit and a cat. She must temporarily take Ichigo's place as leader of the Mews to defend Tokyo from the Saint Rose Crusaders, while juggling her schoolwork and her new job at the Café. When Ichigo returns, she and Berry quickly become friends and she and the other Mew Mews move to her school in case of an attack

From HMR:

Sora just wanted to live a plain, simple life. So what happens when something strange demands to be taken home with her?

Kurosaki-sensei is an isolated science teacher seeking to gain popularity with her students. Watch as she tries to win the hearts of her students!

One-Shot by Sorachi Hideaki(author of Gintama) Originally published as part of the Top of the Super Legends one-shot series, It was included at the end of volume 38

Collection of adult comedy short stories.