Some more references that I've found:
Various episodes:
-Konoka is sometimes seen having the same eyes as Ichijou from Pani Poni Dash (no surprise since Ai Nonaka voices both characters, and most of the Negima!? staff also worked on PPD).
Episode 5:
-During the still of Negi taking the blame of Chamo's peeing on Asuna's sheets, Asuna is seen wearing the same yellow dress that Asuka wore when her character was introduced in Neon Genesis Evangelion.
Episode 7:
-The Triforce from the Legend of Zelda is seen in the "video game" shot of Haruna and Ku Fei's room.
Episode 8:
-The Chupacabra t-shirts that Asuna gives to the twins features a pair of Chupacabra performing the Fusion technique from Dragon Ball Z.