The class overview CG is a good start. Contains at least Lezard, Ikuno, and gender-bent Haruhi. The original release of Act 1 has also Lelouch but he was taken out in the full release, replaced with a more generic-looking guy. The official blog has confirmed another: Ritsu. She was intended to be an original character, but by sheer coincidence resembled Ritsu when K-ON finally aired. Rather than change the design, the developers performed a "retcameo".
Also, the chubby guy in the top right corner looks a bit like Peter Griffin, but it's probably unintentional.
Tea house Shanghai was originally supposed to be a Higurashi reference, but the devs quickly backtracked and made it a Touhou one instead.
After a conversation with Kenji, Hisao mentions a book he's reading a book about "an underground postal system that may or may not exist", a reference to The Crying Of Lot 49.
When Hisao wonders if he's Only Sane Man, Kenji says that he's the only sane man in the school, and as a certain foreign film puts it, "there can only be one!"
It's also possible Kenji was referring to Jet Li's "The One", which has a similar premise.
Hanako is reading a book about "a boy and a tiger on a boat". This is Life of Pi. If you don't scare Hanako away in the library, she'll even namedrop it. At one point, Hanako also reads "Dance Dance Dance" by Haruki Murakami.
When talking to Hanako about a certain book series, Hisao recommends she read the original book, but warns her that the sequels aren't nearly as good. However, he does concede that "The God Emperor" is pretty good.
Hisao picks up a random book in braille while in her room. While he's unable to actually read it, the title (not in braille) reveals it to be "Death on The Nile". Lilly apparently likes Agatha Christie's detective fiction.
Kenji mentions at some point that he sees Shizune at Hisao's door, intending to give him his mail, and how he warded her off with the shine from his glasses.
Another possible reference to the Guide is when Hisao meets Shizune's father Jigoro, and wonders if he avoids to see him, then he also cannot see Hisao, just like the Bugblatter Beast of Traal.
Kenji states at some point: "You're already spending less time here. That's the first thing they do. They'll try to split us up. Divide and conquer. Sun Tzu said that." It is possibly a reference to the Soldier.
In Emi's route, Kenji asks that Hisao deliver his hidden journal to the media if something should happen to him.
When Hisao asks why Kenji is collecting items to maintain a fallout shelter in Hanako's route, Kenji praises him for being familiar with the Protect and Survive booklets.
The WrittenSoundEffects during Hisao and Emi's pillow fight are most likely inspired by the old Batman TV series. WHAM! BIFF! SOCK!
The chapter in Emi's route when Hisao has dinner at the Ibarazaki house is called "Guess Who's Coming... Never Mind".
The description of the second-to-last chapter in Emi's good ending is "Sex, drugs, but no rock 'n roll".
Apparently, Kenji tried to send a letter to LEGO in order to get them to make Dragon Ball themed Lego at age 8, and apparently got a response that they couldn't get the rights to make it.
Hisao tells Kenji that Shizune has the habit of lifting her glasses just like he does, so naturally he concludes that she must be copying him and screams that she could be one of those pod people.
In Shizune's path, Kenji also mentions Sex and the City during one of his crazy rants against feminism.
Early on, Hisao says that when they heard about his arrhythmia, his parents "practically had two hemorrhages apiece," a reference to The Catcher In The Rye, in which Holden says something similar about his parents in the first chapter.
One of the late scenes in Emi's route is entitled, "Hooray forSocks".
Mutou bears more than a passing resemblance to the Tenth Doctor, and seems to think in the same general way all incarnations do.
Misha quotes President Kennedy at one point during Shizune's path. "Ask not what your school can do for you...but what you can do for your school!" This is possibly a hint towards her fondness of American culture.