Though their boxes are nowhere to be seen, Kirino also refers to Saikano and Tengen Toppa Gurren Lagann by (partial) name — "Tengen Toppa 12 Sisters". This is in addition to an actual Sister Princess game box that can be seen in her closet.
In the initial shots of Kirino's closet, a DVD box set of "Sis×Sis" can be seen, referring to kiss×sis.
The preload screen for the otaku website is of two characters from NekoSis, another work by the same author and artist.
"It's not even funny as a joke. Call yourself Psyco Gundam or Big Zam from now on."
That clip from Maschera we're shown features some guy who looks like a cross between Hei and Lelouch (who is apparently called Lushi). The mask he was wearing is reminiscent of the mask worn by the masked men/the Liese twins in Magical Girl Lyrical Nanoha A's.
Yamanashi Ganma? As in Kisaragi Gunma? Or am I mistaken?
And the named company Alice+ is a possible portmanteau of Alicesoft and Nitroplus.
"Siscalypse" carries a few Lyrical Nanoha references, notably the magic circles and "Stand by, ready."
With a Stealth Pun to the fansubbers/torrenters/etc. Unlicensed Blade Works
Kyosuke references the Rance series of games when he told Manami that he'd show her his Hyper Weapon.
While singing along to the opening song to Stardust Witch Meruru, Kirino does Ranka Lee's "Kira☆!" gesture twice. This is possibly also a nod (and maybe a subtle hint about how Kirino truly feels) to Kyousuke'svoice actor having played Ranka's love interest in that show.
The opening title sequence mimics the typical style of eroge openings, particularly when introducing the main characters (this is usually done with the names of their voice actors as well) Or So I Heard.
Actually, Meruru is half a parody of Nanoha, and half a parody of Heart Catch Pretty Cure, because one, the civilian forms of the girls are a parody of Tsubomi and Erika, and the opening parodies the scene in the Heartcatch opening where they are walking to school and talking.
When Kyosuke gets lamped by Ayase in episode 10, he spins through the air in the same way as Taichi does in Cross Channel and Nanaca Crash.
The two games that Kirino wants Kyousuke to buy in episode 12 are Parody Names of actual H-games already in the market, namely as "3D Custom Imouto" being a one-word swap of 3D Custom Girl and "I'd never steal something like Onii-chan's pantsu" (three guesses).
In Episode 12, when Kyousuke finished talking to Saori, she said Nyoro~n
During episode 5, when Ayase is having a... freakout... she yells over and over about lies, and how she hates lying. The next day, what flashes on the screen for a moment? A cicada.