In the manga, Nekonome-sensei claims to be "thirty years younger", thus "seventeen years old", a joke often used by her voice actor, Kikuko Inoue. Yes, the manga shouts out to a voice actor.
Well, it is Kikuko Inoue. She's kind of a legend at this point. The joke takes a new form when she voices Mizore's mother.
In the anime episode Body Measurement + Vampire, when Ruby is playing the doctor, she seems to have been taking fashion tips from Ritsuko Akagi
Chapter 15 of the second manga serialization introduces the magical whip "Belmont", complete with title cover and panel done in the style of an early Castlevania game, which even features Goddamned Bats. The whip's power of magic canceling is identical to that of the Vampire Killer, the whip the Belmonts wield. Except that Belmont doesn't burn/kill vampires with a touch, like Vampire Killer does. Good thing, since Inner Moka is the one who uses it.
In episode 5 the soccer players' shirts are nearly identical to those worn by Nankatsu team
How about in chapter 23 of part II of the manga: Tsukune catches a big-ass phoenix by the beak. Even some minor similarities - after everyone's finished gaping (because the phoenix is supposed to be really powerful), it's getting ready for another go, and someone else steps in and takes it down.
During the school festival, a saibaman can be seen in the crowd.
In Rosario+ Vampire II in Ch 29, In quite possibly the most obvious shout out to Rumiko Takahashi ever, The third dark lord asks Inner Moka to cosplay as Lum from Urusei Yatsura (without telling her what the costume is until after she's wearing it, of course), only because he is One of Us.
Akuha seems to know how to use Nanto Rokuseiken. or at least something that looks like it.
As is only appropriate for a manga with vampires, chapter 31 has a nice little homage to Jo Jos Bizarre Adventure. A few pages later Akuha announces what she wants out of life, and Dio Brando would be proud.
Episode 10 of Capu2 shows us there's a Piranha Plant at the lunch room. It's plainly seen in the background when Kotaro saves Yukari from falling after she slips on a banana peel.
Ah, heck! They somehow managed to sneak Akira in for some reason...
Extremely hard to see in the scanslated chapter online (it's clearer in the Viz translation due to it being easier to get an closer look at it)but in chapter 3 season 2 if you look close at Kokoa's face in the last picture on this page look at the mask she's wearing.
In the same page as the second Akira ToriyamaShout-Out mentioned above, the Handicraft Club (where they have gone to solve Kokoa's "problem") not only has a board reading "Cosplay Club" clear as day (much to Kokoa's dismay), there's also Jotaro's jacket at the door.
Rubi's fight takes place in a corridor that resembles the one where Neo fought Bane/Smith likely because both fights feature electricity.
The "Meaningless End-of-Volume Theater" Omake for Season II Volume 6 includes a scene where the girls adopt appearances based on characters from other series. Kurumu is wearing Odango with the little covers, Rubi has Holo's ears (and tail), and Mizore has on a North High uniform.