Based on the clues we can infer around the black boxes in this proposal for SCP-001 we can infer that the movie script they changed was The Matrix, and that the author they tried to kill was Stephen King. The SK book that most closely matches the revelation that the SCP universe is a fictional construction controlled by horror writers in another universe is, of course, the Dark Tower. In the series, (MAJOR DARK TOWER PLOT SPOILERS) Stephen King's characters are real but he doesn't know that, and they have to prevent his death to save the universe from destruction. However, it's implied that King does not create the universes he writes - he is just a messenger for a higher power. If we extend this to the SCP universe...
SCP-009 is a form of H2O that transmits its anomalous phase transition properties to any normal water it comes into contact with. Ice-Nine, featured in Cat's Cradle, is also a form of H2O that transmits its anomalous phase transition properties to any normal water it comes into contact with, causing The End of the World as We Know It.
SCP-023 is an SCP-ified version of the Black Shuck, a Hell Hound from British folklore.
026 very closely follows the plot of the Goosebumps book, The Haunted School.
SCP-099 is a portrait that causes people who view it to suffer delusions that anything with eyes (and sometimes even things without eyes in extreme cases) are staring at them. This SCP seems to be a reference to Nikolai Gogol's short story The Portrait.
One of the things the vending machine gives out happening to be a bottle of Nuka-Cola.
Single-serving containers of "Insta-Mash", both pre and post-war versions.
Another test result yields "Mr. Q's Cumbersome Soda Bottle". It's a bottle of soda featuring a stopper that interrupts the flow of soda if the bottle is not held at the proper angle. In other words, a Ramune bottle.
Another test involved Glock 17's. On the Very Fine setting, a blaster from Star Wars. The same researcher then tried to use swords to make a lightsaber.
Once an arrow on Very Fine results in a metal one, the researcher is reminded of something and puts it back with a page of Guardians of the Galaxy. The result is a fully working replica of Yondu's one!
"Following the unfortunate, and completely preventable, death of Agent Gallagher" at the hands of SCP-953, any personnel found to have current or prior ties to the "furry" or "otaku" communities are to be immediately reassigned to other projects."
The extended testing log of SCP-1459 has a few termination methods clearly inspired by various works of fiction, helped by the fact that it accepts work titles as termination methods and comes up with creative kill methods from there. Just to name a few:
"I like trains" results in a train running the puppy over at high speed.
"Rage" results in a second puppy that hulks out and kills the first.
SCP-1502, a small robot which walks around and mutilates people's faces, doubles as an in-universe one since it winds up making its victims resemble the appearance of Mr. Feeny and it only identifies as / speaks by playing recordings of Shawn Hunter.
The phrase "Shakes me, makes me lighter" repeated in SCP-1782 is a shout-out to the lyrics from "Teardrop" from Mezzanine by Massive Attack (AKA the opening credits music for House). Doubles as a Genius Bonus considering the music video of that song and the nature of SCP-1782.
SCP-1881 is a shout-out to Polybius, a(n urban) legendary arcade game has a strange psychological effect on players; additionally its stages are modeled after actual classic games:
The "spaceship" stage, could be one of several early Shoot 'em Up games.
Once subjects have found these ears, they will show reluctance to taking them off
SCP-1936: In the middle of a weird prophecy, there is this: "Sheogorath remains, ruling his kingdom of two faces before he himself brings its downfall (...)", which is basically the plot of Shivering Isles, name and all.
SCP-2516 is the Urban Legend of "The Man from Taured", an inadvertent Dimensional Traveller detained in Paris International Airport with a passport from "Taured", a supposed country landlocked between France and Spain's borders. Passing away after years in the Foundation's custody, his cremated ashes were sent in a cart down the train tunnel they believed might've been his portal between their timelines, hoping he could be laid to rest in Taured. After that, a cart with a different urn returned through, this one's note requesting burial in the Principality of Andorra.
SCP-2600 is an Atari 2600 connected to 8 anomalous televisions. The addenda note that the project behind its creation was titled "STELLA", a codename for the system and the name of one of the more well-known 2600 emulators for PC. Also a reference to Game Theory, which hypothesized a connection between Atari and the CIA's MK-ULTRA program.
When SCP-3090 is killed in a game of Tetris, her body disappears and is replaced with Document 3090-B and Document 3090-C. Document 3090-C is a non-anomalous Game Stop Powerup Pro card with Super High School Level written at the top.
SCP-3885 is basically a community ripped right out of Mad Max, but in this case, it realistically shows what happens when a bunch of mutated scavengers with more muscles (and limbs) than brains try to make giant, souped-up desert rigs out of stolen trucks: namely, lots of explosions.
SCP-4503 is Strega Nona's magical cookware. In fact, its depiction in the entry is exactly what happens in the book: someone started the pot and forgot the stop command, causing it to smother the village with delicious pasta.
The incident report for SCP-4950 involves a field agent who used to be in IT and is trained in the occult intervening in a cult's attempt to summon something that rests in the fold between gray goo scenario and eldritch abomination, all the while lamenting about the cult's "poorly optimized" summoning circle. The agent is one Robert Howard.
The second part of the title for SCP-4960 is an obvious reference to Dr. Strangelove. Additionally, Kedesh-Nanaya's deep slumber when Procedure 166-Anahita isn't active is more than a little reminiscent of Sleeping Beauty.
SCP-5420 is inspired by Space: 1999, with elements such as the NASA designation of the anomaly (Meta), character names (Paul, Alan, John Koenig), down to the yellow-orange color space suits being outright references to the show.
Dr Gerald's Personnel File has a note from another SCP operator who mentions loading up "my waifu", his shotgun, with bolo rounds to pay him a visit.
The Cool War: street artists Banksy and Robbo are at least aware of the Mad Artist group "Are We Cool Yet?" and Pico AKA The Snipper has way too much in common with Gamzee to be a coincidence: His seat of choice is a "corpse pile" ("___ pile" is a thing in Homestuck), his art project dumping a ton of the green slime that must never come into contact with dead bodies onto said corpse pile is announced with a loud HOOOOOOOOOONK, and this page shows how he and Mr. Redd interacted - Pico writes timidly with lower-case letters in crayon while Mr. Redd uses a lot of bold/underlines/all-caps written in blood.
The Groups of Interest entry for the Unusual Incidents Unit mentions that another USGOV entity that deals with the anomalous is "Seal Team Bravo Papa Romeo Delta"— translate that from the NATO Alphabet, and you have Seal Team B.P.R.D..
Sloth's Pit, Wisconsin is a Quirky Town where weird stuff happens, called a "Nexus" in Foundation terminology. The Hub for the canon centering around Sloth's Pit names Roadkill County, Oregon as another major Nexus.
72) Dr. Bright is no longer allowed to offer the solution of "Use more guns" to any problem.
73) Despite what he may say and any evidence, no matter how pausible, the SCP Foundation has never and will never be associated with Hogwarts School of Witchcraft and Wizardry, and regardless what Dr. Bright may say, he is not, and I quote, "A real life wizarding tutor"
77) Ctulhu and R'lyeh are not valid reasons to send Pandora's Box to the Pacific Ocean in order to capture them. Futhermore, these are not scps, and I will find the person who decided enter a database file for them.
87.1) If Dr. Bright is found deliberately getting high to get out of paperwork, he is to be placed in a Type 4 cell and hosed down with cold water from a pressurised hose for no less than 5 minutes. Maybe this will teach you that drugs are bad, m'kay?
93) Just because Bright is a doctor does not mean that he is theDoctor, no matter how many British men he possesses.