Misa Kakizaki's light-brown-turned-violet-hair was the only case in the series of an Adaptation Dye-Job getting it right. Akamatsu originally intended her hair to be that colour, but wasn't able to portray it with the tankobon's limited colour palette.
Negi's pactio card number is 496, which is the sum of the numbers 1 through 31. It is also the third perfect number (it is equal to the sum of its factors).
Kurt Gödel was an Austrian-American mathmetician and philosopher. Similarly, "Jack Rakan" is really "Jacques Lacan," with the spelling mangled by round-trip translation.
Chigusa Amagasaki, Big Bad of the Kyoto arc is named after one of Akamatsu's assistants.
As is the case with Keiichi Yamashita, the "3D-jujitsu" practitioner from the Mahora Budokai who Evangeline handily defeated.
The Kiyo-mizu temple seen in chapter 29 is a real temple in Kyoto which is famous for having a mixture of Buddhistic and Shintoistic styles. From the drawings it is very clear that Akamatsu has been there as the drawings are faithful to the real temple and its surroundings.
It was in Love Hina as well, complete with "Jumping off Kiyomizu stage" saying.
Akamatsu likes incorporating famous architecture into his art; check Negima's entry under Real Place Background for more examples.
Many of the Web sites in the series are completely fictional, and several others are Bland-Name Product versions of real sites (e.g. 2channel). The domain of these sites is www.ailove.net, Ken Akamatsu's personal site. However, several real sites have been featured at their actual URLs. For instance, Chisame used the Perseus Digital Library in Chapter 121 to look up information on mages.
Adaptation Overdosed: Negima!, Negima!?, Negima Neo, Negima!!, and assorted OVAs. Thanks to the constant Continuity Reboots, nothing but the OVAs have covered more than a small fraction of the manga.
Dawson Casting: Most people in the Live Action Adaptation seem far from their supposed age.
Doing It for the Art: The tankobon extras reveal just how much effort Akamatsu-sensei and his team put into this manga.
Schedule Slip:"Negima will be taking a break next week" "Negima will be taking a break next week" "Shonen Magazine (which Negima is in) will not be sold next week" "Negima will be taking a break next week" Repeat ad infinitum.
Torch the Franchise and Run: The series' rather abrupt ending is the result of Ken Akamatsu dropping the series in protest against his publisher's attempt to take ownership and copyright of the series away from him. The publishers may have given up quickly, but Akamatsu seemed to have been tired of the series anyway, thus the inclusion of elements that could only be considered spiteful towards the fans, like sinking every Neg-related ship and giving several characters like Chisame completely ambiguous and hotly contestable epilogues... That is, until he decided to tie up some loose ends via his Stealth Sequel.
The Nightmare Circus subplot was planned during the Mahorafest but due to the already extensive plot-line it was scrapped. Given that it kept Zazie mysterious until her reveal in the Magic World, this might've been a good thing.
Judging by Negi's class roster at the end of the series, there were many more storylines that were likely dropped due to the abrupt end of the series.