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 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 Wand: The Thousand Master's staff works this way, as does the ring Eva gives Negi. Straighter examples appear when Yue and the rest of Ala Alba learn beginners' magic.
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.)
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.
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.
Near Misses: stronger character vs. anyone using the time-warping bullets
Neck Lift: 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.
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.
And then there's 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-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.
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.
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.