I will remove this section once I deem the guide will be complete.
Having some personal issues, I put the project on stand-by for now.

Here is some YT videos I took inspiration for references I didn't knew (I don't remember all of them but these were the major ones):

https://en.wikipedia.org/wiki/2001:_A_Space_Odyssey_(film)
-------------------------------------------------------------------------------------------------------
HAL 9000
In the hospital when Dr.Atherton talk to Sam Walker, he do it throught an intercom ressembling closely to HAL 9000.

https://en.wikipedia.org/wiki/A_Few_Good_Men
-------------------------------------------------------------------------------------------------------
Colonel Nathan R. Jessup
In a document, there is mention of a "Colonel J.R. Jessup" which is a reference to the film's main antagonist Col. Nathan R. Jessup played by Jack Nicholson.

Framed Photos
In a house of Keen Sight at the end of Chapter 1, there is two framed photos coming from the film. (Not owning the film I didn't find an upscale image of the second photo).

Lieutenant Jonathan Kendrick
In a document, there is mention of a "Lt. J. Kendrick" which is a reference to the film's secondary antagonist Lt. Jonathan Kendrick played by Kiefer Sutherland.

https://en.wikipedia.org/wiki/Alien_(film)
-------------------------------------------------------------------------------------------------------
Deer Hugger
One of the Deer collectible named "Deer Hugger" got the said creature on its face.

Pinball Machine
A pinball machine parody named the "Xeno" (named after the film's creaature Xenomorph), can be seen in several locations in the game.

https://en.wikipedia.org/wiki/Aliens_(film)
-------------------------------------------------------------------------------------------------------
Apone
One of the H.A.D.E.S. operative is named Apone (as seen on its locker in the H.A.D.E.S. office), like the USS Sulaco Sergeant Al Apone.

Bishop
In a document the supervisor of Keen Sight's Water System system is named "Bishop L. Henriksen", named both after the USS Sulaco's synthetics Lance Bishop and its interpret Lance Henriksen.

Hudson
One of the Keen Sight's street is named after USS Sulaco Private William Hudson.

LV-426
The level where Raven try to escape the Abomination is named ELV-426, like the planet LV-426 where the events of the two first films occurs.

Rebecca Jorden
The scientist who launched a distress call from Aegis Labs is named after Rebecca "Newt" Jorden the sole survivor of Hadley's Hope colony.

https://en.wikipedia.org/wiki/Back_to_the_Future
-------------------------------------------------------------------------------------------------------
Delorean & Flux Capacitor
In the garage near the power plant, there is a unmodified Delorean and the flux capacitor (maybe ready to be mounted).

Fantastic Stories
The "Fantastic Stories" comic book that George McFly readed in his youth can be seen scattered in various location throughout the game.

For Sale
On several wooden boards throughout the game, there is a the time machine Delorean to sale.

OUTATIME
Several GMC Deloreans can be seen with the license plate "OUTATIME", like the film's modified Delorean.

https://en.wikipedia.org/wiki/Back_to_the_Future_Part_II
-------------------------------------------------------------------------------------------------------
Almanach
A magazine similar to the film's Almanach name "Sports Book - 1950-1998" can be seen in various locations throughout the game.

https://en.wikipedia.org/wiki/Deep_Blue_(chess_computer)
-------------------------------------------------------------------------------------------------------
Beat Deep Blue
A parody poster of the book "Behind Deep Blue: Building the Computer that Defeated the World Chess Champion" can be seen in various locations in Keen Sight's streets.

https://en.wikipedia.org/wiki/Blade_Runner_2049
-------------------------------------------------------------------------------------------------------
s99821
There is several cars in the game with "s99821" license plate, which is the same as Agent K's spinner.

https://en.wikipedia.org/wiki/Broken_Arrow_(1996_film)
-------------------------------------------------------------------------------------------------------
Mission: Broken Arch
A poster parody named "Mission: Broken Arch", can be seen the Invader Studios appartment.

https://en.wikipedia.org/wiki/Buffy_the_Vampire_Slayer
-------------------------------------------------------------------------------------------------------
Vampire Slayer
A parody poster called "Vampire Slayer" can be seen in the bedroom of Invader Studios.

https://en.wikipedia.org/wiki/Capcom

Capcom HQ
In a document, there a mention a I-400 submarine leaving Osaka to deliver the "Shujin" to Germany. Osaka is the location of Capcom Japan HQ.

Kazuhiro Aoyama
A plate with "Aoyama Corp. - Japan" can be seen in Keen Sight's streets, this is a reference to Kazuhiro Aoyama, director on Resident Evil 3. He also helped Invader Studios in the early stages of Daymare 1998.

Satoshi Nakai
A plate with "S. Nakai - Art Studio" can be seen in Keen Sight's streets, this is a reference to Satoshi Nakai who worked as creature designer for Resident Evil: Code Veronica and Resident Evil 0. He is also credited as one of Daymare 1998's Enemies Concept Artists.

Shinji Mikami
The creator of the Resident Evil franchise is referenced in a document as "Admiral Shinji M."

https://en.wikipedia.org/wiki/Capricorn_One
-------------------------------------------------------------------------------------------------------
Mars 1978
A parody poster called "Mars 1978" telling to reveal the truth behind the Capricorn One mission can be seen in the bedroom of Invader Studios.

https://en.wikipedia.org/wiki/Christine_(1983_film)
-------------------------------------------------------------------------------------------------------
CQB241
Several cars throughout the game can be seen with the license plate "CQB241", like the film's antagonist Christine.

Christine Garage
The garage near the powerplant at the end of chapter 3 is called "Christine Garage", in addition to have a 1958 Plymouth Fury on its enseign.

https://en.wikipedia.org/wiki/Cliffhanger_(film)
-------------------------------------------------------------------------------------------------------
Qualen
In a Hexacore encrypted file, the head of Hexacore of Internal Affairs is called "Eric Qualen", like the film's antagonist.

https://en.wikipedia.org/wiki/Coca-Cola
-------------------------------------------------------------------------------------------------------
In a grocery store, there is two brands of Coca Cola parodies.

https://en.wikipedia.org/wiki/Con_Air
-------------------------------------------------------------------------------------------------------
AZZ KIKR
Several cars throughout the game can be seen with the license plate "AZZ KIKR", like DEA Agent Duncan Malloy's car.

Cyrus the Virus
A tag in Keen Sight's streets says "Cyrus the Virus", like the film's antagonist Cyrus "The Virus" Grissom.

https://en.wikipedia.org/wiki/Dante%27s_Peak
-------------------------------------------------------------------------------------------------------
Virgil's Peak
A poster parody named "Virgil's Peak", can be seen just in front of Keen Sight's cinema.

https://en.wikipedia.org/wiki/Deep_Rising
-------------------------------------------------------------------------------------------------------
Argonautica Cruise Ship & Finnegan Travel & Co
A poster advertising the Argonautica Cruise Ship by Finnegan Travel & Co, are both a reference to the film's ship called the Argonautica and the hero John Finnegan played by the late Treat Williams.

Deep Falling
A poster parody named "Deep Falling", can be seen in front of Keen Sight's cinema.

https://en.wikipedia.org/wiki/Demolition_Man_(film)
-------------------------------------------------------------------------------------------------------
Deconstruction Man
A poster parody named "Deconstruction Man", can be seen the Invader Studios appartment.

John Spartan in a frame
In the H.A.D.E.S. office there is a low res picture of John Spartan (not sure it is the correct image due to the low resolution of the picture).

https://en.wikipedia.org/wiki/Die_Hard
-------------------------------------------------------------------------------------------------------
Al Powell
A guard named Al Powell can be seen in the beginning. He is a reference to Al Powell, John McClane's radio support.

Dr.Gruber
A character named Dr Gruber is mentionned in one of Hexacore's Encrypted Files. He is a reference to Hans Gruber, the film's main antagonist.

Hard Hero
A poster parody named "Hard Hero" in Japanese, can be seen in one of the hospital's room.

https://en.wikipedia.org/wiki/Die_Hard_2
-------------------------------------------------------------------------------------------------------
Live Hard 2
A poster parody named "Live Hard 2", can be seen in Keen Sight's arcade.

https://en.wikipedia.org/wiki/Die_Hard_with_a_Vengeance
-------------------------------------------------------------------------------------------------------
Die Soft
A poster parody named "Die Soft", can be seen the Invader Studios appartment.

South of the Border
The truckstop near the powerplant at the end of chapter 3 is named "South of the Border", which is a reference to "North of the Border/Nord des Lignes", a Canadian truckstop where the film's climax takes place.

https://en.wikipedia.org/wiki/Dirty_Harry
-------------------------------------------------------------------------------------------------------
East .44
The revolver is named "East .44", which is both a reference to Clint Eastwood and his signature weapon in the Dirty Harry franchise. However the ingame weapon is a Smith & Wesson M629, the chromed version of the Smith & Wesson M29 used by Harry Callahan.

https://en.wikipedia.org/wiki/Escape_from_New_York
-------------------------------------------------------------------------------------------------------
Call me Plissken
A graffiti "Snake Plissken escaped from here" can be seen in several location in the game. Reference to the character Snake Plissken from the film and its sequel "Escape from Los Angeles".

https://en.wikipedia.org/wiki/Event_Horizon_(film)
-------------------------------------------------------------------------------------------------------
Death Horizon
A slightly altered poster of the movie, called "Death Horizon" can be seen the Invader Studios appartment.

https://en.wikipedia.org/wiki/Face/Off
-------------------------------------------------------------------------------------------------------
Face/On
A poster parody named "Face/On", can be seen the Invader Studios appartment.

https://en.wikipedia.org/wiki/Fear_and_Loathing_in_Las_Vegas_(film)
-------------------------------------------------------------------------------------------------------
Fear in Keen Sight
A parody graffiti of the film titled "Fear and Loathing in Keen Sight" can be seen in Keen Sight's streets.

-------------------------------------------------------------------------------------------------------
Death Rides the Forest
A 1933 U.S. Forest Service PSA poster, can be seen in various places.

Smokey Bear
A slightly altered poster of the U.S. Forest Service PSA mascot Smokey Bear can be seen in various places.

https://en.wikipedia.org/wiki/Friday_the_13th_Part_III
-------------------------------------------------------------------------------------------------------
J. Voordeer
One of the Deer collectible named "J. Voordeer", both its name, the machete and the mask are a reference to the film's main antagonist jason Voorhees, its iconic hockey mask and main weapon.

https://en.wikipedia.org/wiki/Friends
-------------------------------------------------------------------------------------------------------
Central Park
A café named "Central Park" can be seen in Keen Sight's street, this a reference to Central Perk, a fictional café brand seen in the series.

P.A.L.S.
A poster parody named "P.A.L.S.", can be seen the Invader Studios appartment.

https://en.wikipedia.org/wiki/Full_Metal_Jacket
-------------------------------------------------------------------------------------------------------
Gomer Pyle
At the beginning of the game, Liev taunts Crane by calling him "Gomer Pyle". This is a reference to Pvt. Leonard "Gomer Pyle" Lawrence, GySgt. Hartmann's favorite whipping boy.

https://en.wikipedia.org/wiki/Jurassic_Park_(film)
-------------------------------------------------------------------------------------------------------
Circuit Breaker
The circuit breaker Liev used to put power back to the Aegis facility is similar to the one Ellie Satler used to bring back power to Jurassic Park.

Computer Screen
The computer next to the Aegis Lab circuit displaying a map of Northfall Islands looks like Isla Nublar map from Ray Arnold's computer.

D-Rex
One of the Deer collectible named "D-Rex" wear a hat similar to the T-Rex's head.

Cryo-Tube
The cryo-tube containing the PL-X 731 is very similar to Jurassic Park's cold storage where dinosaurs embryos are contained.

Shaving Can
A shaving can can be found into the PL-X 731 cold storage is very similar to cryo-compartment consealed into shaving can given by Dodson to Nedry.

https://en.wikipedia.org/wiki/Teenage_Mutant_Ninja_Turtles_(1987_TV_series)
-------------------------------------------------------------------------------------------------------
Pizza Box
Several pizza boxes, labelled "Samurai Turtles Pizza" can been seen in various places in the game.

https://en.wikipedia.org/wiki/Terminator_2:_Judgment_Day
-------------------------------------------------------------------------------------------------------
Deerminator
One of the Deer collectible named "Deerminator" had a part of its face metallic like the battle damaged T-800.

Dr. Silberman
In the second chapter there is an audiolog made by a Dr. Silberman. Reference to the psychiatrist Dr. Peter Silberman from Terminator to Terminator 3.

Judgment Day
Near the basketball playground in chapter 3, there is a graffiti on a wall near a scafolding "August 7, 1997 - Judgement Day. Reference to the said Judgement Day in Terminator 1 & 2, however the date is wrong as in Terminator universe (at least in the first two movies) Judgement Day occurs on August 29, 1997.

No Fate
Several graffitis saying "No Fate" can be seen in Keen Sight's streets. This is a reference to the famous quote "There's no fate but what we make for ourselves".

T2 Pinball
In the sewers in a break room, there is a parody T2 pinball labelled "Sterminator 2.1 - Sentence Time". This both a reference to Terminator 2 and the Terminator 2 pinball machine.

T-1000 in a frame
In the H.A.D.E.S. office there is a low res picture from the T-1000 looking at a silver mannequin after beating the T-800.

https://en.wikipedia.org/wiki/The_Blair_Witch_Project
-------------------------------------------------------------------------------------------------------
Blair Fish & Co
Near Keen Sight's pier, there is a seafood company and warehouse named "Blair Fish & Co".

https://en.wikipedia.org/wiki/The_Blues_Brothers_(film)
-------------------------------------------------------------------------------------------------------
BDR529
There is several police cars in the game with "BDR529" license plate, which is the same as Jake & Elwood Blues' police car.

https://en.wikipedia.org/wiki/The_Fresh_Prince_of_Bel-Air
-------------------------------------------------------------------------------------------------------
Fresh Prince
A graffiti saying "Fresh Prince" can be seen in Keen Sight's streets. This is a reference to the famous show and the said Fresh Prince played by Will Smith.

https://en.wikipedia.org/wiki/The_Relic
-------------------------------------------------------------------------------------------------------
Poster
A slightly altered poster of the movie The Relic appears in the Invader Studios appartment.

https://en.wikipedia.org/wiki/The_Rock_(film)
-------------------------------------------------------------------------------------------------------
General Hummel
A character named Francis Hummel is mentionned in one of Hexacore's Encrypted Files.

The Stone
A poster parody named "The Stone", can be seen the Invader Studios appartment.

https://en.wikipedia.org/wiki/Toy_Story
-------------------------------------------------------------------------------------------------------
Pizza Moon
Several pizza boxes with the logo "Pizza Moon", derivated from the famous Pizza Planet brand in the Pixar universe, can be seen scattered all around the game.

https://en.wikipedia.org/wiki/Tremors_(1990_film)
-------------------------------------------------------------------------------------------------------
Grab-deer
One of the Deer collectible named "Grab-deer" wear a hat similar to graboïds' heads.

Walter Chang's Market
One of banner in the city is a reference to Walter Chang's Market.

UZI4U
There is several cars in the game with "UZI4U" license plate, which is the same as Burt and Heather Gummer's pickup.

https://en.wikipedia.org/wiki/WarGames
-------------------------------------------------------------------------------------------------------
Tic-Tac-Toe
There is a game of Tic Tac Toe on a screen in the strategic room of the Hexacore HQ, reference when David Lightman tricked the W.O.P.R. to play a game of Tic Tac Toe against ifself to show him the concept of futility and no-win scenarios.

"Winner: None"
On another screen, there is also a list of several Keen Sight streets marked as "Winner: None", which is a reference to the W.O.P.R. after playing several Tic Tac Toe games resulting in a long string of draws, run several nuclear war scenarios and each time the result is "Winner: None".

https://x-files.fandom.com/wiki/The_X-Files
-------------------------------------------------------------------------------------------------------
Alex Krycek
One of the H.A.D.E.S. commando is named after Alex Krycek, the FBI Special Agent and Syndicate undercover operative.

Flukeman
The scary Flukeman from the Season 2 second episode "The Host" make as appearance on the cover of a science magazine (more specifically a sketch of the Flukeman on a Weekly magazine from the Season 3 sevententh episode "Pusher"). Plus the article is named "ANOTHER Y-Files".

I Want to Believe
The famous poster "I Want to Believe" from Mulder's office make several appearances throughout the game (althought slightly altered).

Peacock Family
The infamous Peacock Family from the Season 4 second episode "Home", have their named carved on a wooden barrel with a knife planted right next to it.

Skyland Mountain
Skyland Mountain (or Summit) from the Season 2 sixth episode "Ascension" where Duane Barry kidnapped Scully, make an appearance as a part of Keen Sight.

https://en.wikipedia.org/wiki/Xena:_Warrior_Princess
-------------------------------------------------------------------------------------------------------
Pinball Machine
A pinball machine parody named the "Nexa: Warrior Queen", can be seen in several locations in the game.