Genshiken 2 (TV)

The OP (disarm dreamer) animation is an incredibly obvious spoof on the gundam seed series openings, Everything from the animation to the actual song is in the same vein as its gundam seed counterparts (just listen to pride or invoke and then disarm dreamer and you'll see what I mean).

In the first episode, around the eleven minute, we can see two poster : one parodies Code Geass and one Gundam.

During eps 3, you see a digital clock appearing indicating the time. The layout of the clock and the music used is a reference to the television series "24" with Kiefer Sutherland.

In the club room in episode 1, there are two actual Ohno figures on top of the tv.

In episode 2, when Kohsaka and Kasukabe went out together, they are in the "Starbooks Coffee" but in the real world it's Starbucks Coffee

In episode 3, when the female manga club member is looking at the Genshiken's book, the doujin on top of the pile to the left is a Lucky Star book, with Miyuki on the cover. The title is 'iku de gansu', one of the opening lines in the OP of the anime.

In episode 4, at around 3:12 the music you hear is from the game Etrian Odyssey during a monster encounter.

In episode 8, Kuchiki does an overt parody/reference to Sailor Moon, complete with costume and battle pose/speech. He says "I'll annihilate everyone on behalf of the moon!" which is a direct parody of Sailor Moon's famous "I'll punish you in the name of the moon!" speech.

In episode 9, Sasahara states he wants to edit "Beforenoon" which is an obvious parody of "Afternoon", the magazine which serialized the Genshiken manga.

In episode 10, Suzy says lines that were originally from Doraemon, Neon Genesis Evangelion, and Keroro Gunsou, respectively. She is only quoting them.

In episode 11, Suzy says lines that were originally from Laputa: Castle in the Sky, Urusei Yatsura, Lucky Star, and Kimi ga Nozomu Eien respectively. She was just quoting them.

In episode 11, Ohno cosplay as Yoko from Gurren Lagann but some of her dressing is a little different from Ohno

The flashback in the first episode to episode 12 of the first season contains several continuity errors: the characters are sitting in different positions relative to Sasahara, the posters on the windows are the ones Sasahara puts up in episode 13 (OVA 1), the trees outside have leaves (they were bare in episode 12), and the way the lines are voiced (albeit by the same seiyuu) is very different. In context, however, this could all be attributed to Sasahara's faulty memory as he reflects on the reason why they're going to be participating in Comifes.