Art Shift: Many, many times, most noticeably with the chibi Baka Rangers. Several of the characters also had minor changes between manga/first series of the anime to the second for identity purposes.
Ascended Extra: The Narutaki twins, who are hardly seen in the original Negima, have their role greatly expanded early on in the series, being among the first characters to have a Pactio. Chizuru and Natsumi also get this treatment somewhat.
Blessed with Suck: The Neo Pactio system. Each time a partner transforms, Negi will draw one of three cards: an Armor card (the strongest), Cosplay Card (moderately stronger than normal), and a Dud card (absolutely useless); time runs out very quickly and the partner is starving afterwords.
Ayaka's love for Negi, while extreme, never went as far as making stuff such as coffee mugs, t-shirts and other material with Negi's face on them. (This one becomes a bit of a Canon Immigrant as a plane with Negi's face shows up in the manga.)
Asuna goes from a normal girl with really bad grades who sleeps in after her paper route to a girl who suffers from Attention Deficit... Ooh, Shiny! with hyperfocus whose train of thoughts can only be understood by Konoka.
Yuna goes from a GenkiGunslinger to a gun-obsessed tank otaku who just drools over Mana's guns. Whereas the Cheerleaders thought Yuna was over Mana's guns.
Whenever a group of students are possessed by the Star Crystal, they're turned into this. It's taken to the point where the Crystal will say a sentence while cycling through each girl's voice. Quickly lampshaded in the Japanese dub by Chamo.
Chamo: Speak through one person!!
The above is taken to it's logical extreme towards the end, when the Crystal creates illusions of the entire class in order to trick Negi. When revealed, the girls all shout a single sentence, with each girl saying a few words.
Incredibly Lame Pun: Standard fare for Mana and Zazie who grade each other on the quality of the pun or others grade them when the team isnt together. They later start grading ones that they can't possibly hear.
One of the few times this ISN'T done is when they're all in their Suka/Dud forms.
Mundane Made Awesome: Ramen. Eating, cooking, telling the future with it — Takamichi makes it awesome.
Mysterious Protector: A Tuxedo Kamen clone known as the Black Rose Baron is introduced early on. At first, Negi believes that the Baron is his father, but he later finds out from Konoka that the Baron is really his big sister/cousin, Nekane Springfield. If you listen closely you can tell its voiced by a woman
Mythology Gag: Both this show and Negima?! Neo like to play with these. The former spends oodles of time on a one-off chupacabra joke from the original manga, and frequently lampshade Konoka/Setsuna Ship Teases. In the latter, chapter 29 is basically one long Mythology Gag about Konoka and Setsuna's trip to Movie Town during the original manga's Kyoto arc.
In episode 14, during a scene in which all of Negi's students who haven't yet entered pactios with him do so by kissing him one by one, the music that plays is the opening theme from Negima! The animation for that opening ended with each of Negi's students leaning in to kiss him.
Not So Extinct: Asuna spends 24 out of 26 episodes looking the Chupacabra which everyone says doesn't exist; they create a Chupacabra school club and order T-shirts and other items. At the end of the series, she finds one (which she quickly puts to work signing T-shirts.)
Power Gives You Wings: Setsuna's armor pactio card does this unlike her original self which she is half demon and has them naturally.
RPG Episode: Sayo's exploration of the dorm. She gains stats as she scares the crap out of the dorm residents from a top-down perspective like the original The Legend of Zelda. The Triforce even makes an appearance.
Kumā makes an appearance on a sign during the camping trip.
When Eva grows to gigantic size, the reactions of the other characters are almost identical to a scene from the 2nd season of Galaxy Angel.
There's a Pokemon shoutout at one point.
In episode 21 when Evangeline and Chachamaru become mysteriously trapped in a house in the middle of a body of water, it may be a reference to the Gainax Ending of Tsukuyomi: Moon Phase, especially considering that like that show's protagonist Hazuki, Evangeline is a vampire. Evangeline even turns up in a cat costume at the end of the episode, while Hazuki frequently wore a Cat Eared Headband.
The status screens in ep 26 greatly resemble the interface in Etrian Odyssey.
In one episode, Mana can be seen cleaning a gun◊. That gun happens to be the positron rifle◊ from Neon Genesis Evangelion. The design is slightly different, but the plate reading "JSSDR" is nearly identical to the one reading "JSSDF" on the rifle in Evangelion.
Shoe Slap: Asuna throws both her shoes at Eva before throwing a boat.
Spotting the Thread: Towards the end, the Star Crystal creates illusions of Class 3-A in order to trick Negi into jumping into an abyss. When Negi is reluctant to do so, fake!Eva quickly tries to pull a Heroic Sacrifice, telling Negi to jump while she stalls the monster chasing them. Real!Asuna (the real Class 3-A is watching the events unfold) quickly calls fake!Eva out for her uncharacteristically noble behavior, which is what tips Negi off that he is being set up.
You Are Number Six: At the start of the series Negi calls his class by their number; in an illusion later on, their number is tattooed on them, changes places and is always in frame.
In the "normal" opening sequence (there are a few variants of this) the girls are nearly ALWAYS depicted with their number next to them. This even occurs when their face isn't shown. The only exception to this is when the girls are walking at the beginning (some are, some aren't) and Asuna when she's running through the desks with Negi.
Wingding Eyes: Asuna gets hearts when she gets the game Zombie Rider: The Son-In-Law.
Wiki Walk: Asuna does this a lot. Only Konoka can explain the route she took to get there.
A-Cup Angst: Anya, just like in the original, but here it's played with even more.