Magic Contract Romance: Negi notes that there is a trend where Mages are known to marry their Minister/Ministra Magi.
Magical Incantation: Typically in unfamiliar languages, such as Latin, Greek, Sanskrit, and archaic Japanese.
Magically Binding Contract: Pactio is the most obvious, but least straight, example. A straighter invocation occurs when Fate and Godel each try to make Negi sign one which would have the power of a geas.)
Magic Dance: Most Konoka's healing magic involves dances.
Magic Land: This would be the near-literal translation of Mundus Magicus.
Magic Missile Storm: One of the most basic and common offensive spells is Saggitta Magica (Magical Arrows). They come in a variety of elemental types with different properties, and almost every mage is seen using the spell at one point. Near the end of the manga Negi fires off a volley of 1001 lightning Saggitta at Fate, who notes that while Saggitta Magica is a low-end spell Negi has scaled it up so much that it's essentially the same as an anti-army spell.
Magic Staff: He carries a staff most of the time when doing magic. It serves as a focus for his spells and he also uses it to fly in a manner resembling a Flying Broomstick. It also is a Memento MacGuffin since Nagi was the one who gave it to him.
Anya uses one of these as opposed to Negi's staff. Using a wand to cast instead of a staff or other focus is apparently considered childish. They also don't work as well.
Sceptrum Virtuale looks like a magical girl toy, but it actually gives Chisame hacking abilities.
Magitek: Chao's Deadly Upgrade and Powered Armor, as well as Chachamaru's very existence. Oh, and a magic gun. And then there's the Paru-sama (a Goldfish-Style Aerofish with a high-propulsion-pentagram-18-prayer-spirit engine and anti-pirate military-grade armaments.)
MasculineFeminine Gay Couple: Konoka and Setsuna. Konoka is a very girly and cheery Ojou with healing powers while Setsuna is a serious swordswoman with some Bifauxnen looks who is determined to protect Konoka from anything. This aspect of their relationship is emphasized in some occasions where they dress up and Setsuna ends up wearing male clothing to contrast Konoka's elegant dresses.
Since Negi is so young, most of the girls don't feel embarrassed around him. Anya, though, is willing and capable of sending him flying - but only if he lets her.
Meido: A favorite of Evangeline and Fate, and apparently standard uniform for Magic World slaves.
Mental World: During his Magia Erebea training, a copy of Evangeline yanks Negi's mind into a magic scroll and creates a world for him to train in.
Me's a Crowd: Negi attempts to make a single copy of himself using a traditional Japanese magic that animates a paper doll, with which he is unfamiliar. Eventually he succeeds and goes away, but afterwards the four failed paper copies also come to life.
Mid-Season Upgrade: Chachamaru gains one of these after her Gadgeteer Genius creator Hakase gathered the observed battle-data of the previous arc. Among a few new weapons and a speed upgrade, one major aesthetic improvement has her concealing her mechanical joints with softer, more realistic skin. She still has a set of antenna ears on her head, so its not hard to figure out she's a robot.
Mind over Manners: Nodoka's ability is limited to just mind reading, but it's specifically noted that she's probably the one with said artifact simply because she's the one least likely to abuse it.
Misplaced Accent: In the English dub, Negi speaks like an American attempting the I Am Very British Received Pronunciation accent, not in anything like a Welsh accent.
Negi's absent mother gets absolutely no mention until we finally learn that his mother is/was Princess Arika Anarchia Entheophysia. He didn't know either.
Mrs. Cocolova was turned to stone while Anya was away. She dusts her off regularly.
Mobile Shrubbery: Nodoka uses this to quietly approach Natsumi, Makie, and Yue all talking about Negi.
Monster Mash: Negi's associates include a ghost, a vampire, a half-bird demon, and a dog demon. On the other side, the REALLY monstrous-looking bounty hunters are later seen casually relaxing in the same baths as Negi and company.
Negima!'s left-field ending; the gateport incident in Vol. 21.
A more minor one comes when Kurt Godel explains Negi's lineage and then gives Negi a We Can Rule Together offer. An otherwise serious moment is made funny with the inclusion of an RPG-style 'Yes/No' dialogue option.
Negi uses this almost continuously early on. He constantly infuses himself with magic so he can keep up with the girls as they sprint to school. It's more obvious after he temporarily seals his powers which makes him totally unathletic. He also tried to help Asuna do her paper route faster by giving her a lift on his flying staff, but it didn't quite work out.
Kaede uses her ninja techniques to do things like hunt fish.
Mutually Exclusive Magic: Ki and magic are incompatible for the vast majority of people. For those people that can use them together (only three so far have been shown), it becomes a Yin-Yang Bomb.
My Kung Fu Is Stronger Than Yours: Not only do the major characters spend almost all their time off-screen either training or sleeping (and have been doing so for years), the training itself is a frequent plot point on-screen — especially if it's Training from Hell.
My Parents Are Dead: When Asuna takes Negi for a bath, this comes up. Negi immediately feels bad for mentioning it but Asuna doesn't make a big fuss out of it. Given how old she is, her parents, if any, are likely a distant memory.
Mysterious Protector: The manga shows Negi thinking of his father this way, even placing himself in danger hoping to get him to appear.
Myth Arc: Negi trying to find his father. The result isn't pretty.
Naked Apron: Setsuna's version of Cosmo Entelecheia involves Konoka dressed like that.
Naked First Impression: Since Chizuru and Natsumi find Kotaro while he's in his dog form, he's naked when he first meets them.
Negi's father does this to a demon in the flashback to the destruction of his village, and finishes it with a nice squeeze too.
Later, Negi himself pulls it on Tsukuyomi when she foolishly tries to assault the ship with him on board.
Nerf Arm: Setsuna wields a broom during the Tournament Arc to get around a restriction on bladed weapons. Shinmeiryuu techniques do not seem to actually require a weapon, so she could have even gone barehanded.
Never the Selves Shall Meet: Negi royally screws this up during the Mahora Festival, requiring some quick damage control from Kotaro of all people.
Never Trust a Hair Tonic: A female variation, when short-haired Ako thinks she should grow her hair out to be more attractive. A (not so) helpful denizen of the magic world promptly gives her a magic hair-growth potion, which works perfectly for all of a minute before the hair begins to engulf her.
New Year Same Class: Taken Up to Eleven. Negima's class doesn't change at all, despite there being around twenty other classes in the grade. Hand-waved before it happened; it was stated that Mahora doesn't split up its classes.
Newspaper Dating: A short-term version is used in the Mahora Festival Arc to find out that the team's stay at Evangeline's resort lasted for much longer than thought.
First tournament fight in the Mundus Magicus arc. Negi and Kotaro dodge a really big attack combo... only to appear leaning on the big guy talking about how much that would have hurt.
When Kaede is going up against Sanders in the tournament semifinals, he tries to instantly end the fight by crushing her with gravity magic. She appears right behind him, chatting about how the one being crushed is just a clone.
When Yue trips over a tree root in the Library Island arc and twists her ankle, she implores Negi to leave her. Negi refuses and tries to carry her, but since he has no magical augmentations, he fails. Kaede picks up Yue and effortlessly carries her out.
At the climax of the aforementioned arc, Negi attempts to stay behind because otherwise the elevator won't move due to the weight limit being exceeded. Asuna overrides his decision and tosses the magic book they were looking for instead.
No Romantic Resolution: We never find out who Negi liked. We know he didn't like Asuna during the sports festival and he didn't end up with Nodoka, Yue or Evangeline while Chisame is apparently a hikikomori and Makie is still fruitlessly pursuing him. Not many plausible options after that. The answer wasn't given until years after the ending through the Stealth Sequel: it was Chisame.
Nosebleed: Given the amount of fanservice and awkward moments, this trope is surprisingly rare. Most of them involve the class representative, and random background characters.
The Nose Knows: Chamo uses a pair of panties to track down a pair of enemy girls who are dozens of kilometers away with pinpoint precision.
No-Sell: Chisame is completely immune to the fake Cosmo Entelechia because it works based on how dissatisfied the target is with their life. Chisame is right where she wants to be. When she learns this, she's predictably insulted, which in turn makes Makie insulted, who was also immune.
No Smoking: Chamo's cigarettes were winkingly labelled "chocolate" in the first anime.
Not a Date: Setsuna denies that her outing with Konoka is a date, despite everyone, including Konoka, treating it like one.
Not Just a Tournament: There's a tournament whose hidden purpose is to gather evidence of the existence of magic and flood the media with it.
Not Quite Flight: Kotaro can't fly, but his shadow hounds can, and being made of darkness, he just forms them into the shape of floating wheels attached to his feet so he can run through the sky.
Not So Different: From Fate to Negi and most recently from Tsukuyomi to Setsuna.
Not the Fall That Kills You: When Negi's group warps back an entire week they emerge a few thousand feet in the air, but their fall is cushioned by Negi's wind magic.
Not What It Looks Like: After Asuna wakes up from a dream where she remembered her time with Ala Rubra, she stumbled across Setsuna and Konoka in the middle of making a pactio. Given that the UST had begun to escalate at this point, all Asuna sees is her roommate about to kiss her friend and bodyguard. Note that while Setsuna totally panics when Asuna comes, Konoka isn't the least bit flustered.
Evangeline herself is a blue-eyed vampire who is Really 700 Years Old. It was recently discovered that she herself is also a creation of the Lifemaker; an experiment on the concept of indestructibility.
Ocular Gushers: An anime staple, though when the characters are seriously crying, it's not exaggerated.
Odango Hair: Fumika has them and can be seen as part of the page's picture.
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 Christmas story about Fuuka and Fumika, it is mentioned but never shown.
Oh, Crap!: Jack making shit puns before confronting Fate's minions during Godel's ball. He says he has to go take a dump, and then tells Fate that everyone has to wipe their own asses. Truly, the shithas hit thefan.
One Dialogue, Two Conversations: When Negi asks Asuna to accompany him on a trip to search for traces of his father as his magic partner, Asuna misinterprets it as a love confession, as do Yue and Nodoka, who overhear it. Haruna doesn't, but she does enjoy the ensuing hilarity.
One-Gender School: Mahora seems to separate the genders, but apart from 3-A it's never elaborated on.
One-Hit Kill: Time-displacement bullets. (Interesting in that it's not a "kill" in the traditional sense, but tactically there's little difference.) Also, Code of the Lifemaker has this effect on natives of the Magical World.
One-Sided Arm-Wrestling: Negi vs Ku Fei. At first it seems like Ku Fei's brute strength will win but then Negi takes it seriously and completely beats her.
Subverted later on; after Negi single-handedly wipes out a gang of bounty hunters, the leader starts muttering about revealing his true form. Negi gives him a mean look, and he goes back to cowering on the ground.
The Only One Allowed to Defeat You: In chapter 314, Fate is revealed to have survived, and is fighting Quintum to protect Negi's comrades. Because only he is allowed to defeat his rival.
Only Six Faces: Ken's art style is essentially this. A lot of character from both genders have the same face.
Only Smart People May Pass: The end of the Baka Ranger arc has the titular five girls answering test questions to facilitate their escape.
On the Money: Buying out slaves = one martial arts tournament. Actually an inversion: It makes perfect sense for a martial arts tournament to have around one million Drachma as a reward, but not so much for that to be the exact price of the slaves' debt.
Opera Gloves: During chapter 282 Negi shows up to the group meeting with long gloves up to his elbows to hide his Magea Erebea marks.
Orwellian Retcon: How old is Negi, chronologically? Well, the initial magazine releases said he was born in the summer of 1993, making him about 9 years old in the prologue. The bound volumes changed this to simply "1994", consistent with his earlier admission that he's only 10 if you use kazoe, and Word of God reportedly has him at about eight and a half at the start of the series.
Evangeline: Hurry and whip it out, boy! Negi: But Evangeline-san, we already did it, it's too much! Evangeline: I told you, call me master.
By the way, the payment was sucking blood from his arm.
Later on, Chachamaru nearly causes Chisame's head to explode with this poorly worded statement about Negi's martial arts training.:
Chachamaru: I have been serving as Negi's partner every night and he seems to be happy about it.
Overly Long Tongue: A Negi golem created by Haruna has a 23.5 cm tongue. She first states that "it" is 23.5 cm long, causing some of the girls to think of... something else before she clarifies she meant his tongue.