Evangeline's training resort is a clear allusion to the Room Of Spirit and Time, except that one hour in it equals one day as opposed to one-day-equals-one-year.
When Dean Konoe explains the world tree's power — specifically, its wish granting power, it is mentioned that it could not summon a pair of panties; there's even a silhouette of Oolong visible in the background.
During the Mahora Battle, one student is shown firing his weapon like a Kamehameha (he's even saying "Kameha...").
After Negi's students first see him use Magia Erebea, one of them asks if he just used the Kaio-ken.
In chapter 292, Haruna imagines that Fate Averruncus and his allies will be waiting for Negi throughout several floors of the royal mausoleum, with Koyomi and Tamaki on the lowest floor, Shirabe on the next floor up, Tsukuyomi on the floor above that, Dynamis on the next one above that, and finally Fate himself on the top floor. Yūna comments that "That is way too cliché! What is this, Game of Death? Muscle Tower? Yeah, right!"
Back in the early days of the manga, when Negi and Kotaro teamed up for the first time to fight Graf and the Slime Sisters, this exchangehappens.
During the first summer break, when the twins are showing Negi around the school, they directly compare the World Tree to Yggdrasil (The one from Dragon Quest, not the one in Norse Mythology that it's named after)note Also it makes sense that they would need to explain that to him, as at the time that chapter came out, none of the Dragon Quest games had been released in Europe.
A chapter titled "Rakan at 120%" is a shout-out to Younger Toguro from YuYu Hakusho, who infamously stated he would use a certain percentage of his power, but his true true power was 120%. Another possible allusion is with the match between Negi and Rakan which rather resembles Yusuke and Toguro's final engagement and more...
Chisame's personality, infatuation with computer stuff, and pactio all scream Corrector Yui.
When Nodoka uses her artifact on Mei in Chapter 141, the diary entry read "Eeeek! C-C-Could that be the Legendary Death No--!? I mean that artifact that reads"
The interior of Ala Alba's "goldfish ship" looks nearly identical to the Bebop.
Chapter 261: Negi and Ku-Fei's arm wrestling match shouts out to a Sylvester Stallone movie named Over the Top. Especially Negi shifting his grip.
Not to mention that during the whole thing, Ku Fei is dressed almost identically to Chun Li.
Chinese Girl Ku Fei's personal requirement that only a man who is stronger than she can kiss (or marry) her echoes the cultural imperatives of the Joketsuzoku from Ranma ˝ (and Red Sonja, for that matter). Some fans are claiming that she is a Joketsuzoku, and that Negima and Ranma take place in the same universe.
The manner in which cards are drawn from the girls in Negima!? is similar to the way swords are drawn from people in Revolutionary Girl Utena.
Also during the tournament arc, there are several panels of online discussion concerning the techniques being used by the combatants. One of the comments is "We have a STAND USER!"
Negima!? has a number of references to Pani Poni Dash!. Most noticable is that the Chupacabra Club resembles Becky's research room.
A number of the Pani Poni Dash! references have to do with Konoka having the same seiyuu as Ichijou, right down to Konoka wearing the same Indiana Jones outfit that Ichijou wore in a couple of episodes
Similarly, in the last normal episode of Negima!?, each of the girls are displayed in an Etrian Odyssey type status screen.
Kurt Gödel is named after an Austrian mathematician/philosopher most famous for his incompleteness theorems, which state that there is no consistent formal theory in which all arithmetic truths can be proven.
Speaking of Rakan and mechas, when he unleashes his skyscraper-sized sword, he references it as the Ship Cutting Sword. That's right, the guy has his own Zankantou.
The "Code of the Lifemaker" and the names of Nodoka's adventurer friends are all references to the works of James P. Hogan.
The series quite possibly makes Shout Outs to its own doujinshi. In Chapter 264, Negi comments about wanting to keep Chisame by his side, with her curt response being "...don't say stuff like that with a straight face. You'll get yourself stabbed by a girl one of these days." In Negimaru, a very.... ecchi doujin series by Studio Kimigabuchi (the same studio behind the acclaimed Neon Genesis Evangelion doujin RE-TAKE) that predates the chapter by several years, Negi ends up getting stabbed... by a crushing-on-Negi (amongst other things) Chisame.
It's apparently referenced again in chapter 338, making Chisame look like she's going to be a bit of a stab-happy Yandere. She even threatens to stab herself and Chachamaru afterwards!
When Negi first fights Evageline, he is seen carrying around a Caster.
Actually, that was first from a Martial Arts Movie movie called "Shaolin Wooden Fighting Men" (or something like that) featuring Jackie Chan. Tekken referenced that for Mokujin, and it's repeated here.
There are numerous references to Akamatsu's previous manga, Love Hina, not the least of which is Setsuna's school of swordsmanship, the Shinmeiryuu, which is the same as that practiced by Motoko Aoyama. In fact, Akamatsu has confirmed that Motoko and her elder sister Tsuroko are indeed — as many fans had suspected — making a cameo appearance in the flashback scene in Vol. 4.
Add to that, that Eishun is confirmed in a Audio Drama to be born Eishun Aoyama (taking his wife's last name when they got married).
The Cursed Urashima Blade appears in a flashback between a young Setsuna and a woman closely resembling Tsuruko. In both Love Hina and here the sword is said to have almost wiped out the Shinmeiryuu in the past. What's more, the same chapter hints that Tsukuyomi apparently stole the sword and is currently wielding it, and if that sword is indeed the cursed blade, it could be what's driving her insane, given the effects of that sword as shown in Love Hina.
Not to mention the fact that Tama appears three times. Once on a random beach, once drawn by Haruna and on Chizuru's Pactio outfit.
Also, Naru and Seta can be seen in the background during the Mahora-Budokai at one point.
Much of the aesthetic designs in Negima (especially weapons, clothing, and magic emanations) greatly resemble motifs used in the Guilty Gear and Blazblue series. Heck! Rakan himself appears to be Sol Badguy with blonde hair and a dirty/funny personality.
And in chapter 348, Zazie channels Arakune, while she herself is dressed up as a spider.
In Chapter 258, when Nodoka is describing magically created alternate planes, her explination goes something like this: "Alternate planes...traditionally, places "not of this world" where spirits and the souls of the dead can be found. Famous Japanese examples include the Dragon Palace, Ryuugujou and Takamagahara, the land of the gods...and more recently, mysterious towns with public baths found at the end of a tunnel."
Devil May Cry. Here and here. Badass Longcoat with folded sleeves just like Dante's coat in 4 and a pair of guns that resemble Ebony and Ivory◊ (although the white one doesn't look like Ebony, the black one shares the same model with Ebony and Ivory, a modified M1911).
Another Devil May Cry reference (possibly): here Setsuna cuts the guy's armor, which falls off only after she click-sheathes her katana. Jut like Vergil likes to do.
Negi's students have compared Ostia to Laputa numerous times.
Shiratori Yuri was cast as Kiryuu Nanami in Revolutionary Girl Utena, who was obsessed over by a boy named Tsuwabuki. She was later cast as ghost-girl Aisaka Sayo in Mahou Sensei Negima!, who (in the anime) died trying to protect her little sister's tsuwabuki garden.
The Shinmei Ryu sword school from Love Hina exists in both, and Setsuna's origin flashback in the manga shows her from a distance being escorted by two women who are probably the Aoyama sisters from Love Hina. Also, the Mad Scientist creator of the Robot Girl comments on how they outsourced for the programming code of her AI, and one of the programmers was from Akamatsu's first manga, AI Love You, explaining how it is that Chachamaru has emotions. The character Mei has the same given name and character design as Naru's half-sister from Love Hina. While in the anime she had the same family name as Naru, the manga never stated, as she was only in one chapter, hinting that the two may be the same character.
It really veers into Continuity Overlap at some points, especially with Love Hina, as the whole Shinmeiryu sword school crossed over. The most recent chapter even explicitly mentions both Motoko's family, and a specific exorcism technique has plot relevance in both Love Hina and Negima.
Then there's Nagi defeating the Lifemaker with what appears to be a Shoryuken!
Forget that. How about Chibi Chui giving Negi a Shoryuken at Governer Kurt's ball?
In the chapter of Negima that introduces Sayo, the girls of the class are enlisted to hunt the ghost girl, who they think is evil. What weapons do the technology department of the school lend them? Proton packs.
In one episode of Negima!?, 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.
In chapter 75, Negi and crew visit Hakase just as she is about to run some tests on robot-girl Chachamaru. She gives them all a fright, as she's wearing several tons of science equipment. In Del Ray's translation, the following line of dialogue pops over Negi's shocked face: