Pay attention to the voice screaming; it's the same actress who played Cecily the first time around.
In episode 7 Sena mentions that she decided to stay awake a little later to see the ending of the game she had just finished, the ending went on for another four hours and she mentions how touched she was and how she couldn't stop crying when the character Mikane said Goal at the end, fans of Air know exactly how she felt.
The Pari-den manga Kodaka reads in Chapter 13 features a character with a ripoff of Grevil de Blois' hairdo.
Turns out the game they were to have voice roles in — Heaven of the Eastnote "Higashi no Heaven" is an obvious pun of "Higashi no Eden" — is actually an eroge, and everyone is not happy that Rika didn't tell them. Cue Rika's reaction:
In an extended reference to Kobato's voice actress's well-known role as Kuroneko, "Kurogane no Necromancer", the goth-loli anime Kobato watches, closely resembles "Maschera", Kuroneko's own favorite show.
Sena, who is a brother away from being an older Kirino, mentions that her favorite character from that show was "Mer". Kobato instantly tells her that the correct nickname is Meruru. Stardust Witch Meruru was Kirino's favorite show.
When Yukimura bumps into Kodaka (who deliberately did so in order to catch his "stalker"), the former gives him his wallet with a decoration of six coins arranged in two rows of three, alluding to his namesake, the famous samurai Sanada Yukimura, who used it as his family crest.
In the second episode of Haganai NEXT, Rika names among her yaoi anime I Can't Believe My D*** Is This Cute and Rub! Nyarlo-san (complete with tentacles). Sena's eroge sounds suspiciously like something Kirino would play... and then the third episode is called "My Little Sisters Are This Cute".
Episode 2 has Sena watch a film inspired by Kuso Miso Technique
In episode 5 of Season 2, Sena talks about Mayo Chiki!, and the show even includes bland ripoffs of scenes from it, such as when Jiro finds out that Subaru is a woman.
In episode 7 of Season 2, Rika make a pretty obvious reference to Dragon Ball Z.
Funimation translated the name of Kobato's favorite show to "Fullmetal Necromancer". Coincidentally, Kodaka's actor played Barry the Chopper.
In S1 E12, Rika fawns over Yozora's newly cut very short hair, then notices her purple eyes and has an instant realization, runs out of the club room and comes back with a white golden-trimmed ensemble. Yozora, having to wear it, thus totally looks like Lelouch from Code Geass.
In Season 2, Sena plays another Galge over several episodes, and while the school uniforms are white, the characters seen are totally Rise and Yukiko.
When was the last time you saw a group of highschool students do a movie, led by a self-absorbed overly-perfect director, helped by a Deadpan Snarker and about a witch and a girl strangely often seen in a maid dress fighting a bunch? Oh, right.