From ADV Manga:

The prestigious Aoi Academy caters to an elite collection of young magic users. But 17-year-old Kazuki Shikimori is a student who passes muster in name alone. He is the youngest in a long line of sorcerers, but the family's long-running talent for the black arts ended with this average student. That doesn't stop the female population of Aoi Academy from vying for his attention, though! His impeccable DNA will start a teenage war of lovesick girls!

In the middle of an escape, Lilith, the head of a group of thieves, is injured. She is rescued by the young aristocrat Jean Rhode, but in exchange for being nursed back to health, he demands that she pay him with kisses!

Includes the short story Nil no Koi Mahoujin (Nil's Magic Circle of Love):
Nil, a 5th grader in an academy of magic falls in love with Kowloon, her scary-looking upperclassman. Will she be able to pluck up the courage to ask him to the academy’s dance party? She might need magic to give her a helping hand…

From Evil Flowers:

A short oneshot about the Demon of Love; the Incubus who, in order to become a Full Demon, needs to feast on the essence of 10,000 women. However, the last woman he chooses is actually a boy?! So, the Incubus decides to live with the boy, until he has completed his quest to become a Full Demon. It’s not shounen-ai, just a comedy.

A failed youth pill turns the pretty Pozsi, a resident witch of FairyLand, into a little girl. She is dating the handsome and kind Prince Yvrin, but how will he react when he sees his beloved Pozsi as a child? Is there a cure?

This series references many popular fairy tale stories by mixing in its own little twists and showing these popular tales from a whole new perspective, the perspective of a witch!

From Project Kurai Ryu:
Young Kai has been passionately idolizing Ginta ever since his heroic battle in the War Games of six years ago. Since then, ARMs have become a common thing, Guardians especially! Kai himself doesn't have one though, and dreams big of being able to get an ARM like Ginta's! When his caretaker, the old ARM-smith that took him in after his parents' deaths, sends him out on an errand, he is attacked by a bandit from "chess"! In his escape attempt, he finds more than he bargained for when he comes across Babbo! But, now with Babbo's awakening, the fake ARMs are going out of control! Is it Kai's turn to save MARHeaven following in his hero's footsteps?

This is a cute dialogue-less little story about a young girl and an inquisitive little feline friend.

Fujieda Miyabi's The Caged Miko and the Whimsical Witch depicts a romance between-- you guessed it-- a miko and a witch. In the first chapter, Letty, the witch, ends up playing the knight in shining armor to Tsumugi, a young woman magically bound to her family's shrine.

Miko = priestess

Mei no Naisho revolves around the life of the title character Mei Haruna, an effeminate young boy who was raised by his witch mother as a girl, and always thought of himself as female. His mother was the only family he had, so after she died, he transfers to an all-girls high school and resides in the school's dormitory with his familiar Abel, who is talking cat, and his roommate Fuuka Honjou, who is a member of the public morals committee.

Shortly after arriving at the school, his new friends discover after a magical display in the dormitory community bath that he is actually male, though this comes as quite a shock to him despite him being aware of the physical differences between him and normal girls. Despite him being found out, and after some helpful intervening of the perverted student council president, the principal of the school decides that he can stay at the school.

The next day, Mei comes to school with Fuuka and apologizes for hiding the fact that he was a witch, and informs the others how he is apparently male. The other students quickly accept him as one of their own, and are impressed how he can use magic.

[From ADV]:

Orphen, the tough-talking sorcerer-for-hire, is putting his wand-wielding skills to use for quite a price, but with a boneheaded companion and a wide-eyed pupil tagging along, they can’t help but attract a little trouble! Magical mercenaries are all around, and the hair-triggered Orphen is no stranger to a good fight, so he’ll have to cast his spells in record time to stay in the game of magic in Orphen.

A one-shot manga. It’s an action/comedy story about a woman named Tyria who is a maid in disguise, but in reality she is sort of a counter-terrorism operative. It's up to her to stop a hostile takeover by pirates on an airship using only cooking items, like a frying pan, cutting knives and even a fork as apart of her deadly arsenal.

Set three months after the first series.

The story place between the first and second seasons. Fate is having some strange dreams product of the long exposure to magical girls anime and for being apart of her girl for too long.

From JMS:
Based on the Sega Saturn game of the same name. The story follows the most troublesome class of the Magical School on the island of Yen and their adventure to understand each other and protect the island and school from the Vile Tribe.

In a vast world, Emma, a girl with something lurking inside her, meets the magician Shion!!! What is the "Magico" ritual that will bind them together?! Even if they risk their lives to tread a path of thorns...!!

Humans are a despicable lot, committing sin after sin, filling the endless boundaries of the underworld with tortured souls. Now, it would seem, Hell isn't so endless after all, and it has become dangerously close to filling, and then overflowing into the human realm. Princess Lucuha sees this imminent disaster and has a plan: save Hell by making humans decent again. Of course, the angels can't simply allow demons to roam freely on Earth, and they do their best to stop Lucu and her dastardly plans.

Nominated for the 12th Annual Osamu Tezuka Culture Award.

Yukimi, a chubby junior high student, discovers a magical dumbbell that can transform her into Miyuki, a beautiful and slender young woman in a revealing costume. But she must do battle with an evil three-star chef who tempts young girls with calorie-rich treats and dubious weight loss products, and keep her identity secret from her family and schoolmates.

There is a sequel, "Miracle Dieter Miyuki VV." It is being serialized in Shimbun Akahata. As of Oct 2009, there are no plans to publish it in tankoubon format.

A collection of one-shots:

Vol 1:
Magician
Fairy Tale
Cocona
Plue's Adventures Pt. II

Vol 2:
Bad Boys Song
Magic Party
Christmas Hearts
Fighting Group Mixture

A sea prince wishes to have Christmas under the sea. Can his butler make his dream come true?

From Anime New Network: Zushio was to be king and promised his sister that he would become king (on penalty of death). Unfortunately for him, his empire was overthrown and now he's a wanted man. A girl has the misfortune of running into Prince Zushio and becomes tangled in his plight. Adding to her misfortune, Zushio is not quite right in the head, but hey, at least he seems to be immortal.

During a flashback, an interviewer inquires Kuzumi Taiga, a prospective student for Seinagi Private High School, on what he would do if he could use magic, during his entrance interview. He replies, "take over the world", with an outburst of laughter, from an attractive girl, following his answer.
After the entrance exam, the school rejects his application; although he recalls almost nothing after this event, he does recall the girl, and believes the cause of his school of choice rejecting his application involves her.
Wandering around outside of the school the next day, Kuzumi tries to enter, but an invisible barrier blocks him. A teacher, Mr. Hiiragi, confuses Kuzumi for a student of the school ditching class and pulls Kuzumi into the school through the barrier.
Seinagi Private High School is actually a magic school and Mr. Hiiragi has just accidentally pulled Kuzumi, a teenager with no magical skill, through the barrier into this school.