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troperville

In the pilot episode of the anime, when Kirino shows Kyousuke her large stack of H-games, several real-life titles can be spotted in said stack, including (but possibly not limited to) School Days, Summer Days, and Cross Days, Akane-Iro Ni Somaru Saka, and Da Capo. Naturally, all of these titles have varying degrees of Brother-Sister Incest.
Though their boxes are nowhere to be seen, Kirino also refers to Sai Kano 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 X Sis' can be seen.
The preload screen for the otaku website is of two characters from NekoSis, another work by the same author and artist.
Bajeena... really, Saori?
"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."
"Just as planned."
Kate/Starry Night
- 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's voice actor having played Ranka's love interest in that show.
In the manga, Misaka Imouto makes an appearance.
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.
The Show Within a Show Meruru is clearly a Shout Out to Lyrical Nanoha, complete with her seiyuu and the wave motion guns.
- 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.
- Episode 15 fits in one last Nanoha Shout Out with Stardust Witch Meruru The Movie 1st.
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.
Some (all?) of the games that Kirino wants Kyousuke to buy in episode 12 are Parody Names of actual H-games already in the market, such as "3D Custom Imouto" being a one-word swap of 3D Custom Girl.
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.
Sena "Mystic Eyes" apparently have mystic eyes that can see the death of anything digital. When she takes off her glass, they are as good as dead. No...deader than dead.
A poster in the games clubroom says "Rosen Jungfrau". ''Jungfrau'' just happens to mean "maiden" in German...
There are games called "Imouto 2" and "Final Sister IV" in Kirino's closet, which reference Mother 2 and Final Fantasy.
From the first DVD commentary of the Vol. 7 BD is this little gem:
Kyousuke (as Lucifer from Maschera): I don't see anything wrong with the mascot character turning into the villain halfway through the show. It's a common trend these days.
*cut to a thought bubble showing Kyubey*
The Games Research Club room in episode 13 has copies of hobbyist boardgames Stronghold and El Grande on the shelves.
Probably Crunchyroll sub only (from season 2 episode 1):
Kirino: "I sense a god-tier game!"
The game that Kirino plays in the second episode of Season 2, Love Touch is a parody of Love Plus
When Kirino takes Ria to Akihabara in Episode 4 of Season 2, there's a brief close-up of a cabinet filled with Sword Art Online figures.
In the second anime series there is a Gal Gun poster on the wall of the clubroom.