From Intercross & Shoujo Crusade:

Chika has always seen Murasame-kun as a rival who manages to constantly piss her off. While wondering out loud to herself, her sister whom overhears Chika, gives her a perfume necklace which supposedly able to capture a guy's heart. The next day, Chika bumps into Murasame-kun and spills all the perfume. As she begins to apologize, he suddenly asks her out?!

From Anime Waves:

Meet Shizuki Maku - to say she looks "above average" would be a slight overstatement, but it's especially bad compared to her older twin brothers, the high-school heartthrobs Retsu and Tetsu. She always wondered whether or not she really belonged in her family, but things take a shocking twist when her brothers plant the suggestion that they may not be related after all.

Now she's supposed to pick one of them to be her boyfriend, all the while defending herself from all the other girls at school who want to keep her "brothers" for themselves! Life isn't easy when you're the ugly duckling!

Sonnan Ja Nee Yo received the Shogakukan Manga Award for shoujo manga in 2006.

From Shoujo Crusade:

Miyako's living her life diligently following rules, just as her deceased father wanted her to. But one day Azuma Koutarou sees her play guitar and blackmail her to join his band. How will she face it up?

There's also three extra stories that are unrelated to the main one.

Tatsuhiro moved to Tokyo to attend an art school and start his new life. In his new room, there’s a small hole in the wall. At first he can see nothing through the small hole, but one night, through the peeping hole, he saw a girl. That’s how his new life starts.

For fighting and humour fans Jo Pae, a not really sane boy, in our modern days, he wants to become emperor of Korea... His first step when he enters high school is to become the leader of the strongest school there is. No one expecting it, he actually takes down all of the school's yankees. Jo Pae is now the enemy to kill! All rival schools wants his head whatever the means!

Without doing much research on the school or surrounding areas, Hibino Ryouichiro picks an art school in Hokkaido. Tricked by the school advertisements, he goes to the campus only to find out it is a desolate and cold campus. The only glimmer of happiness for Ryouichiro are the girls on campus. Just hours after meeting Kisaragi Riho, the cute girl on campus, she seduces him only to find himself outside naked after she is done with him. Feeling heartbroken and used, he finds comfort in Aso Tomoe, who lives on the floor below at the dorms. Although it is freezing outside, it is hot underneath the sheets for Ryouichiro.

Rinne, a huge fan of Buddhism, was searching for a "monk-type," a boy as calm, intelligent and diligent as Lord Buddha himself, when she set her sights on a young, handsome monk-in-training, Yuuryou. She soon learns that this kid, out of his robes, is not her dream boy, but a shallow, irresponsible lady killer who goes by Yura. Is Rinne going to give up on her fantasy, or is there more to Yura than meets the eye?

From Shoujo Crusade:

1-3) Lovers in Conflict
Because of her sister who suddenly ran away, Sagiri ends up getting married in her place. Her husband is hard to understand and is a bit of an S. What will happen to their married life?!

4) Wild Rose's Crown

Vampires have evolved and don't rely on human blood anymore. They now co-exist secretly as normal citizens even though they are still feared and discriminated against by the society. So what happens to a female vampire trying to live a normal school life when she meets the most popular boy in school and accidentally nips his neck?

From MangaHelpers:
Before they enter high school, the boys Meguru and Shou are whining about the fact that neither of them has a girlfriend. A strange, large-breasted woman shows up, claiming that she will fix their problem, and kisses Meguru. This odd occurrence is pushed out of the boys' minds when they meet up with Souko, a friend from elementary school, who is going to be in their high school. She's grown up into a pretty young girl, and it seems like the boys might have a shot with her!
That evening, Meguru realizes that the strange kiss may have had more meaning than he thought: he's turned into a girl! He convinces Shou and his mother of his identity, but no one has any idea how to turn him back. Now he's going to have to learn how to be a girl and let go of his hope of dating his cute childhood friend Souko. What will happen to his hopes for a popular high-school life?

During the summer when everything seemed gloomy I met Sensei and he changed my view on things. The only good trait that Azami, the bashful girl has is that she is honest and diligent. The reason why she kissed him and told him not to forget about her was because she wanted to change herself. During the new school term, the two of them meet again. This time it is at school as student and teacher...

From SCX-Scans:
Though it was a bit strange, three people ended up meeting. One, who looks younger than her age and able to see the supernatural. Another who is possessed by a "Yamanko" which refers to "Yama no ko", or a mountain child. She was possessed due to her bloodline and due to the possession, she has superhuman abilities which she can call upon. Finally, an awkward person who enjoys writing poems. Coincidentally, the three are also classmates.

The manga is separated into 3 story arcs with close to none relation with each other's characters.
Volume 01-13: Video Girl Ai
Volume 14-15a: Video Girl Len
Volume 15b: Video Girl - Complete Story (about Video Girl Haruno)

Video Girl Ai [From Viz]:

High-school student Yota Moteuchi is so unpopular that his classmates have given him the nickname "Dateless." So it's no surprise when the love of his life, Moemi, is not interested in Yota but instead is in love with Yota's best friend, Takashi. Yota turns to a video rental shop for comfort, but little did he suspect that the shop was magical and that the cute girl on his rented tape would pop out of the television and try to fix his ruined love life!

From Aerandria Scans:
Our protagonist, Hikaru, is a member of the astronomy club at her school. On one beautiful starry night, she encounters a tall boy with blonde hair that looks almost white. However, he turns out to be...?!

1) Solely S, Absolutely M
Mamiya has gorgeous looks, terrific grades and outstanding sports reflexes. He’s very popular with the girls in his class, but seems to have no interest in them whatsoever. Sawako is the only girl who treats Mamiya like a slave. She thought there’d be no change in their relationship, but…!?

2) Jitter Bug
When Akane's mother died, she thought she was all alone in the world. Then she found out that her father is still alive and that she has three brothers. What will she do when she finds herself falling for her younger brother?

3) My Dear Cat
Hosoya Mizuki is a university student who has a boyfriend. One day on the way back from school she sees a beautiful cat with one blue eye and one brown eye which seems to mesmerize her. What will happen to poor Mizuki when she will meet a handsome guy with one blue eye and one brown eye and what about her boyfriend?

4) Bet!!
When she secretly took a picture of Saeki-kun, the no.1 popular guy on campus, she witnessed a scene she really wasn’t supposed to!? A bet has been made by him that if he can make her fall in love with him within a week, she'll have to delete that picture... who will win this bet?

5) Love Planetarium
Satoko Fukaya is heartbroken after being dumped by her boyfriend, because she was transferring to another school. While crying she is suddenly pulled into the planetarium by Nanasawa Kouki who seems to have taken an interest in her.

Extra) M's Dejection
Sawako continues to treat her boyfriend like her slave, resulting in Mamiya thinking about breaking up.

Randou Masashi, a self-centered, brash karate star, was the victim of a horrific bus accident that left him comatose, his face terribly disfigured by extensive burns.

Genius plastic surgeon Dr. Manabe saved Randou's life and went to work on his face, gradually reconstructing it based on a photograph found in the wreckage of the bus. But in a cruel twist of fate, the photo that the doctor used as his reference was not a picture of Randou, but of Rina Kurimi, the girl whom Randou has a crush on!

Ten-year-old prodigy Negi Springfield, has just graduated from magic academy, and in order to become a master mage he is sent to Japan to teach English at an all-girls middle school. But Negi has a bigger dream than just becoming a master mage. He wants to find his missing father, "The Thousand Master", the strongest mage that has ever lived. And he soon finds that searching for his father wont be as easy as he first hoped. In fact, it pushes him and his students into life-or-death battles that decides the fate of millions.

Recently rejected Saki Momota is having a hard time getting over her first love. While picking up her younger brother from school, Saki bumps into Akai Ryuuichi; the class delinquent who's rumored to be able to shoot laser-beams from his eyes. Could this day get any worse?

Riding high on the memory of a boy named Hikaru with whom she spent a day during her last year of grade school, Megu went through middle school without romance. Now that she's a high school student, she has decided she is finally completely over her first love and can look towards the future. But! Megu meets a pretty girl on her first day of high school who gives her a big hug, and her name is Hikaru?!

Note: this manga is currently on hiatus due to its author's copyright infringement. There has been no notice since June 2012 about its re-appearance.

Not particularly good at sports, not very popular, and not very good at school, Naoki's middle school years are filled with video games and erotic books. But one day, a cute girl called Iroha appears, claiming to be his daughter from 20 years in the future. Apparently, in the future magic has been discovered, and she has come back in time by magic to protect her beloved papa from a dark future.