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 6 of Season 2, when serving Kodaka his coffee, Sena uses the spell 'Moe Moe Kyun'.