Aborted Arc: Toward the end, many plotlines had to be cut short due to the manga ending prematurely.
The Nightmare Circus, which might have finally given Zazie some character development, was cut due to the Chao arc taking more time than Akamatsu expected.
There was apparently supposed to be a story during Christmas following the Magical World arc, where Fuuka and Fumika would meet two animals who turned out to be magic princes in disguise that the two would eventually marry. Also, Fuuka and Fumika would have made their Pactios with Negi during this time. The events did happen and are still mentioned, but were never actually shown.
Saving Nagi from the Lifemaker. Nagi appears alive and well in the final chapter, and it is mentioned that he was saved from the Lifemaker through the effort of Negi and his 31 students, and healed by Konoka's magic. However, like with the Chrismas story about Fuuka and Fumika, it is mentioned but never shown.
Adjective Noun Fred: Mahou Sensei Negi(ma) (Magical Teacher Negima). Although the protagonist's name is "Negi", not "Negima", the "ma" is there to make a pun regarding a dish involving green onions by the name of negimakinote And yes, we know that the dish's name is suspiciously similar to a hypothetical Portmanteau Couple Name of the protagonist and a particular member of his harem..
Aesop Amnesia: Setsuna has to learn over and over that it's okay for her to both want to be happy and to want to protect Konoka. She learns it at the end of the Kyoto arc, during the Mahorafest tournament, gets an Evil Counterpart that makes her angst about it again and post Magic World she still doesn't get it.
Age-Inappropriate Dress: Happens on both sides of the spectrum, from the girls' frequently donning loli bodies and clothing to the Akemi-esque way Eva lounges around in outfits that are not suitable for a (seemingly) ten-year-old girl.
Air Jousting: A frequent element of the series' often high-flying magical battles.
Air Whales: The standard aircraft of the Mundus Magicus, probably because blimps were too mundane. They also come in various other fish-like shapes.
Alchemy Is Magic: Alchemy has shown up in Negima — specifically, the back of volume 21 has about two pages of text describing the history of alchemy and its relationship to "ixir", as it's called in the Magical World.
All Part of the Show: The Mahora festival, when several thousand Muggles were roped into fighting an army of demon-powered robots and mechas under the pretence of a giant role-playing game. Of course, the weapons used were only harmful to modesty. Also, the fight at Cinema Village. The comment "Is this for a movie?" was commonly seen in the background. This was used in the Magic Worlds as well, especially during the fight with Fate's minions in Ostia. The comment "Are they doing a movie?" is often seen in the background, said by various demons, anthropomorphic animals, and other magical creatures.
Alternate Character Reading: Spell names are written in kanji, while their Latin/Greek/whatever pronunciation is shown in furigana. The later anime replicate this by usually having the characters say the Japanese reading while the foreign pronunciation is said simultaneously in an echoey and quieter back track.
Alternative Calendar: The Magical World has a separate calendar, probably because it's Mars. Which does have a different orbit around the sun, after all.
Always in Class One: They're in class 2-A, then move to class 3-A early on. Justified as Mahora Academy does not do class shuffling.
Amusing Injuries: This is the guy who wrote Love Hina, after all, although it's a bit less prevalent here due to the vastly increased likelihood of not-so-amusing injuries post-Genre Shift.
And I Must Scream: The fate of nearly all the "puppets" of the old Cosmo Entelechia. Since they keep regenerating and are protected by powerful barriers, Eva froze everything else around them which keeps them trapped but conscious for all eternity.
Arc Number: Prime numbers seem to be very important to magic, especially when it comes to the "arrows of whatever." Those are usually cast as prime numbers (or 1). In particular 67note how many million mages there are on earth and 31note the number of students in Negi's class tend to pop up regularly.
Art Shift: Humorous — Makie in the infirmary after her "vampire attack".
Ass Shove: A Running Gag is Chizuru's attempts to test out a folk remedy for fevers, which involves shoving a spring onion up the sick person's assnote as if having a fever wasn't bad enough already. Kotaro and Natsumi are understandably terrified of her. She finally gets to do it in chapter 348. This doubles as a Stealth Pun since a spring onion in Japanese is "Negi"
Attack! Attack! Attack!: Rakan has a tendency to do this, but unlike some characters who use this trope, he generally tends to get away with it sheerly due to his power. This is also how Fate's minions usually operate, and it hasn't gone too well.
Author Appeal: Ken Akamatsu is really into Cosplay, and rarely passes up opportunities to dress the characters in various costumes.
Awesome, but Impractical: The pactio cards allow telepathy between users — but in addition to a limited range, it can be blocked very easily. As Negi puts it, "Isn't a cell phone easier?"
Babies Ever After: As of chapter 355, Fuuka and Fumika were one of the first from Class 3-A to marry, having married twin boys, and both had one daughter each. Chizuru, running a day care herself, seems to love spoiling them.
Ala Alba qualifies as well, as evidenced during the governor's ball, among many other occasions.
Badass Family: Negi, Nagi, Chao, Arika and Asuna. Some of them benefit from Royal Blood magic. If we really stretch, Chachamaru is also a part, given that she considers Chao to be her parent.
Also apparently Lifemaker. Which would make Fate also a member in a sense since the Lifemaker created him
Badass Normal: Surprisingly enough Nagi qualifies, saving Arika from a pit full of monsters without being able to use his magic.
The same can be said for Evangeline — even at her weakest, without her magic and using only the strength of a ten year old girl, she can still toss around full grown fighters using pure martial skill perfected over a century.
Bad Future: The Eight Days Later arc. Chao's future is likely another example, though Mana claims that the tragedy she's trying so hard to set right is no worse than any of the little tragedies that happen every day. Mana turns out to be totally wrong; the disaster is the complete collapse of the Magic World.
Balloon Belly: The result of Makie "helping" Negi prepare for Evangeline's training.
Played with in the Negi vs Chao battle. One would expect the battle to be won by overwhelming power and Heroic Resolve, but here it's decided by superior battle experience. While Chao's spell was more powerful than the one Negi used, Negi's spell had a shorter incantation and covered about two-thirds of the distance between him and Chao before she was able to launch her attack, immediately putting her on the defensive and critically over-straining her artificial magical abilities.)
Subverted in Negi vs. Rakan: Negi pours all of his magical energy into one gigantic attack and taunts his opponent into doing the same for a contest of strength. Instead of launching his attack, Negi absorbs both his own spell and his opponent's blast and uses the assimilated power to wale on Rakan.
Bears Are Bad News: On the contrary; Chief Mama one of the nicest people in Mundus Magicus... so long as you're on her good side.
Natsumi has a thing for Kotaro, who is most oblivious and views her as a sister but has the classic shounen protagonist Jerk with a Heart of Gold thing going for him. Since the former is an immature Tsundere and the latter is a kid, it develops slowly.
In-Universe example, played absolutely literally in the first chapter, which features Asuna getting stripped twice in front of Takahata. Despite the fact he's known her since she was a little child, in chapter 1 is the result when Asuna gets Negi to read his mind to see what he thinks about her.
Also, Takane's constant Clothing Damage has become a running joke. Everyone just says "Ohh...the stripper" when she introduces herself, and even she's started thinking of herself this way on chapter 165.
After Rakan died, he came back to life through his fighting spirit. Then he did more or less the same thing again after he'd been killed a second time.
At least two of Negi's Pactios qualify as this:
First was with Chachamaru, proving that flesh and blood are not requisites for a soul — possibly by sheer force of will.
The other was with Ayaka, of all people, proving that Power of Love can cause a Pactio Backfire if left unchecked. Despite her lack of magic power, her love almost made her the dominant member of the contract.
BFS: Asuna and Setsuna, but Rakan takes the title with his Battleship Slicing Sword. No prizes for guessing what he uses it for.
Less-straight examples of the trope: Kaede's Fuuma Shuriken, Chachazero's butcher knife (she's less than a foot tall, making the weapon-to-wielder ratio pretty high), and Ku Fei's pactio staff — which can grow to gigantic proportions. Also the bound swords used by Ariadne Valkyries, which are closer to spears.
Negi can throw Big Freakin Lightning Spears at people now.
Big Bra to Fill: The live action adaptation didn't quite get some of the girls' proportions right.
Black Comedy Rape: Typically subverted, i.e. when Setsuna and Negi are talking about avenging Asuna's honor when they find her naked and trembling. (She was actually tickled into submission after Fate's Petrification only worked on her clothing.)
Black Magic: There's a Deadly Upgrade explicitly called "black magic" in the manga, mostly because it's fueled by dark emotions. It's perfect for mopey worry wart Negi.
Blank Face of Shame: After Asuna's tragically unexpected and sudden death at the end of the first animated adaption, Konoka is shown sitting alone, her bangs obscuring her eyes and the rest of her face a near-blank.
During Misora's hilarious attempt to attempt to deny her identity, big glowing letters appear above her head proclaiming her name. In chapter 110, "Geh, what's with this caption!? Shush, shush!"
Bloodless Carnage: The series generally adhered to this until the beginning of the Magic World arc. Negi gets impaled by a stone spear, complete with enormous blood loss and the obligatory Blood from the Mouth.
Blood Oath: Impliednote Directly stated in Del Rey's English translation, but it's unknown if this is canon to be the preferred way of forming pactios when kissing would be...unpleasant.
Breast Plate: Both played straight and interestingly subverted. While within the manga canon, Asuna is occasionally given armor that fits this trope, some of the side artwork includes her in very fetching, but still perfectly normal, armor.
Negi Springfield wears a bunny costume during a part of the festival arc. While he is wearing the outfit, his normally serious behavior is replaced with childish enthusiasm, and other characters comment on how cute the outfit makes him.
Nodoka sometimes wears a bunny backpack as a cute accessory to her adventuring outfit.
Cards Of Power: The Pactio Cards provide the recipient with personality-based magical powers, which given the Magister's power, can actually be pretty powerful themselves. Anything from a Magical Computer to a giant weaponized paper fan to a mind-reading book are possible.
One of the only two weapons used by the robot army after the Tournament arc is a laser that only destroys clothing.
The accompanying unsealed demons are bound by "scientific devices" that restrict their powers to the same.
A clothing eating octopus appears briefly to sexually harass the poor Meta Girl.
The Flans Exarmatio spell exists solely for this trope. Negi tends to cast it by accident whenever he sneezes, and a magical all-girls school that features later uses it in an athletic broom contest. It's technical use is to disarm opponents, but it seems to have a very vague idea of what constitutes a "weapon".
When Fate attempts to petrify Asuna during the Kyoto arc, her magic cancel renders her immune to its effects. Her clothes, however, were not protected, and promptly shatter when she moves.
Asuna eventually becomes so used to being a victim of this trope she's built up an immunity to Defeat by Modesty.
In Chapter 277, Yue gets her clothes damaged by a beam that pierced through her and Emily. Rather than treated as fanservice, this is treated as a plot point due to the fact that only Yue's clothes disintegrate while Emily herself disappears.
Confessional: The girls and Negi spend two chapters going to a confessional, manned by a disguised Misora. They unload their anguish, from Genki Girl Makie's worry about having no worries to Negi's deep existential angst, in passing by Setsuna's questions about kissing girls (this is for her to have a pactio and not sexual in nature... probably.). None of it sounded like a true confessional session, of course.
Continuity Lockout: The Ala Alba and Another World animated adaptations assume that viewers have read the first 23+ volumes of the manga, as they were released alongside them. Anyone watching just the anime would be quite confused.
Conveniently Coherent Thoughts: Averted with Nodoka - when she reads minds with her artifact she has to ask what she wants to know to cause them to think about it.
A more subtle example is Fate. Yes, THAT Fate. He will dress up his Amazon Brigade in Meido clothes whenever he can (and does the same to Anya at some point), and when he captures Asuna, he puts her in a really skimpy gown.
Also Kaede. Her pactio kiss involves a look that can best be described as predatory. Then she held that kiss for a few panels and giving Negi a rather deliberate Marshmallow Hell immediately afterward.
Rakan vs. almost anyone. There was the gladiator match, where he took out two high-ranking fighters with a massive punch that left a giant indentation of his fist in the ground. Also when Fate's partners all came at him at once at full power... it was all over in one panel that started with the words "Five minutes later."
Code of the Lifemaker. It's hard to fight someone who can turn you into scattered flower petals with a word. Unless you're Jack Rakan, in which case you can just conjure up metal replacement limbs when your own get erased. And write yourself back into existence through sheer force of will.
Kaede, Setsuna, and Mana all get their butts kicked by Poyo, of all people.
And this seems to be the norm for Fate's minions, who, along with the aforementioned incident with Rakan, suffer setback after setback during their battle with Negi's group — Koyomi's streak of bad luck continued after Ako and Yuuna double-teamed her, Homura's powers were almost entirely sealed, and Tamaki transforming into a dragon didn't help her any.
Chapter 330: Revived Cosmo Entelechia (all 3 generations, minus Fate/Tertium) delivers one to Negi, Fate and Ala Alba.
Eva vs pretty much anyone. Unless she decided to go easy on you to let you stand a chance. Chapter 333 Eva oneshots the entire Cosmo Entelechia minus the Lifemaker
Colonel Sanders vs. Kotaro. Despite his best effort, Kotaro isn't able to inflict any damage to his opponent whatsoever. Although the reason Kotaro wasn't able to inflict any damage despite landing hits was because Colonel Sanders was cheating. He wasn't actually in the ring, he was using split body technique from outside the ring and replacing his double whenever it got injured. Which had the bonus of effectively working as a Teleport Spam, since the doubles could appear wherever in the ring and the one it was replacing vanished as it appeared. That said, with as much of a power difference as there was between Colonel Sanders and Kotaro, Colonel Sanders probably could have curb stomped him even if he hadn't been cheating.