This list the various media that mention Negima, intentionally or not. There isn't a whole lot, but some of quite surprising.
Hyperdevotion Noire: Goddess Black Heart
There's a level devoted to Negima's world tree. It first references Yggdrasial, the tree from the Dragon Quest series that the World Tree in Negima was based off. The reference is furthered sealed by the talk of rumors that confessing under the tree will ensure your love.
In chapter 222 of the Air Gear manga, Negima's manga is brought up on pages 1 & 17. Apparently, the author of Air Gear is a fan of Negima's author, Ken Akamatsu.
Oh! Edo Rocket
There is a reference to Negima in the 22nd episode of Edo Rocket where an "anime about a ten year old wizard" is mentioned. What really makes the scene is that is breaks the fourth wall by mentioning the script-writers who worked on the English dub of the second season, which coincidentally is the voice actress playing the role. The man at the end is also played by the same voice actor of Negi.
Hayate the Combat Butler
In the manga, Hayate the Combat Butler in chapter 148, on pages 9-11, the manga references Negima's roster, fit with a few nods to the details. Funnily enough, Hayate, student no. 20, shares the same spot as Kaede, who are both voiced by the same voice actor in Japan.
ef: Tale of Memories
In the anime series, ef: Tales of Memories, there's a part in episode 6 where various school uniforms are shown. The Mahora outfit from the second TV season of Negima!? is referenced. Both these shows were animated by Shaft.
In episode 9. when going on a date, Chihiro and Renji go to an arcade. In one of the claw machines, a Motsu plush can be seen making an appearance.
So Long, Mr. Despair
In episode 1, during specific shots, there are characters with hairstyles resembling Setsuna Sakurazaki and Kazumi Asakura.
While visiting Komori's home in episode 2, Fuura offers her dolls. When the camera zooms in, you can see they resemble the cast of Negima.
Episode 2 , when in Tsunetsuki's ex-boyfriend's apartment, a certain shot shows a nod to the green amphibian, Motsu, from the second anime series, Negima!?
There's a brief shot that references the classroom layout of class 3-A in the Negima!? adaptation in episode 4. It even includes certain hairstyles and other characteristics of the characters.
At the end of episode 4, there are panty shots of Kaere Kimura, who is voiced by Yu Kobayashi, who also happens to be the voice actor of Setsuna Sakurazaki. As you may notice of Kaere's panties, there is a crude drawing of both Setsuna and a chupacabra. It's drawn by Yu Kobayashi. Due to the voice actor's "unique" art style, it's a running gag to use her drawings in shows she voices in. Her drawings have been present in Negima as well.
When at the convention, several groups can be seen carrying Schichimi and Motsu bags in episode 7. In addition, about midway through the episode, "Pi Kid" is seen wearing a Schichimi shirt. Later in the scene, the design changes to Motsu.
Seen in episode 9, there's a shot with three scrolls at the top of the classroom that read "Chu - pa - T" is a reference to the chupracabra T-shirts Asuna and Negi's allies are seen wearing through the Negima!? series. "Negipa", which is written on the chalkboard, is a nod to the Negipa (or Negima Party Book) series released for the manga.
In the 2008 horror movies, Mirrors, a Negima wallscroll can be seen in Michael's room with other anime posters. This is actually an official piece of Negima merch released by Great Eastern Entertainment.