The Laughing Man is a reference to the Salinger story of the same name
Togusa becomes increasingly despondent that he hasn't heard from the other members of Section 9 for months. He reads ''Catcher In The Rye" and then tries to assassinate Secretary-General Yakushima. For those who don't know, it's the book Mark David Chapman was reading right before he killed John Lennon.
Additionally, the Laughing Man's logo has scrolling text that reads "I thought what I'd do was, I'd pretend I was one of those deaf-mutes." The line is a verbatim quote from its protagonist, Holden Caulfield.
When seen in person, the Laughing Man's clothing also matches the book's protagonist; when remaining incognito, he wears a a red hunting cap, and when disguised as a patient he can be seen holding a baseball mitt with poetry written on it.
A subtle example: In the Laughing Man's library near the end of the series, Motoko's hand can be seen moving over the phrase "Fuck you" written on the railing; in the book, Holden says "You can't ever find a place that's nice and peaceful, because there isn't any. You may think there is, but once you get there, when you're not looking, somebody'll sneak up and write 'Fuck you' right under your nose."
In episode 12 "Escape From" a little girl tells a Tachikoma a story called "The Secret Goldfish", a short story that Caulfield's older brother D.B. writes.
Also in episode 12, "Go See Bananafish" can be seen on a poster, which references "A Perfect Day for Bananafish", another of Salinger's stories.
In episode 22, the Major quotes The Catcher in the Rye by referring to Wilhelm Stekel, by repeating his line "The mark of the immature man is that he wants to die nobly for a cause, while the mark of the mature man is that he wants to live humbly for one."
Night Cruise in its entirety is a shout out to Taxi Driver.
The hostage situation in the Chinese embassy is closely modeled after Nakatomi Plaza in Die Hard.
Saito's flashback episode POKER FACE featured a number of references to Full Metal Jacket. Much of the episode draws parallels with the sniper scene in Full Metal Jacket, from the baiting tactic, to the reaction of the angered teammates, to even the names of some of the Redshirt Army (Mother = Animal Mother, An African American named Snow = Snowball) The show even lampshades it all when a character claims Saito's story was all taken from a movie he'd seen once.
The Matrix was inspired by by the first GitS movie, and when later the series was created, it in turn took many cues from Matrix.
"A Modest Rebellion" is one to French New Wave movie "A Bout de Souffle."
And "Angel's Poem" is to "Wings of Desire."
The killer's MO in JUNGLE CRUISE is practically taken directly from the woefully overlooked cyberpunk film Strange Days.
The episode may also be an homage to The Silence of the Lambs, since it's about a serial killer who preys on women and skins them alive. Note the moths crawling on the bodies of his victims.
As mentioned above, one of the Blade Runner references is to the Enhance Button scene. Togusa's voice commands for the computer are even identical: "Enhance 32 to 50".
"Automated Capitalism – ¥€$" begins with Fem paraphrasing the first sentence of The Communist Manifesto.
"Automated Capitalism - ¥€$" includes a reference by Togusa to Charon, the Greek ferryman who took souls across the River Styx: As the clean-up crew takes away Fem's target, Togusa places one of the coins on his chest and says,"Use that to pay the ferryman."
In the original Japanese he refers to Sanzu River, which fulfills an almost identical purpose in the Japanese mythology.
The credits to the Tachikoma Days in 2nd GIG is reminiscent to Dig Dug.
Actual Shout outs:
The abduction/denial of abduction by Blindfold Ivan is a painful shoutout to the North Korean abductions in the Cold War and how pro-Communist politicians in Japan denied their existence.
Togusa's official appointment as the second Section 9 squad commander is another painful shoutout to how salarymen/women work long, paying jobs and the problem of not seeing their immediate families due to their time spent on work to be the main breadwinners.