A couple to Alfred Hitchcock. The plot of "Double Down" is based on Hitchcock's Strangers on a Train, with both the film and the novel getting a mention. In "Tick, Tick, Tick," taxidermy is referred to as Norman Bates' favorite pastime. "The Lives of Others" is a direct homage to "Rear Window", a fact that is lampshaded by several characters in the episode (later, it turns out that the "killing" was staged and the whole thing really was a homage to the episode, even in-universe).
A subtle nod to Hitchcock; the picture behind Castle's writing desk is a down-shot photo of a square spiral staircase, similar to the staircase shots from Vertigo.
When asked what they call perps, some of the names that the officers answer with are Skeksis and Sleestak.
In "Ghosts", they mention an old oil tanker bombing that crippled the captain. Who was the captain? Why, one Captain Pike. Many of the Castle crew are Star Trek alums.
In "Deep In Death", Beckett discusses how she sometimes visits Little Odessa (Brighton Beach, Brooklyn). When she was Hana Gitelman on Heroes, she tended to be in Odessa, Texas.
From the same episode, Castle grants Alexis permission to see Fame with her boyfriend "but I have dibs on A Christmas Carol." Alexis' actor, Molly Quinn, did voicework for the film.
In the season 2 premiere, Castle asks the coroner if she wants some music, because she's taking a fingerprint from the inside of a glove and he says that in CSI: Crime Scene Investigation they do it to music.
Anyone who follows Nathan Fillion on Twitter probably squealed with pleasure when in "The Double Down", he slipped in his catch phrase "Bam, said the lady", and again when he made the puntacular offshoot "Blam, said the lady" in "Last Call".
Kyra: Out of all the murders at all the weddings in all the cities in the world, you walk into mine.
Quite a few to Casablanca, actually. In one episode, Castle is considering starting up his own bar, and trying to think up a name. His mother suggests "Rick's Cafe Americain". Castle says "That's much better than my idea: 'Castle-blanca'."
In "Den of Thieves", upon walking on Castle's poker lesson for Alexis, Castle's mom references Casablanca with a similar joke:
Martha: "I am shocked, shocked, to find gambling going on in this establishment! [Pause] Deal me in."
In "The Third Man" Esposito asks Castle and Beckett "why are you so obsessed with some motherfreaking snakes on a motherfreaking plane." Sound familiar?
Though probably not a shout-out per se, the baseball-themed episode "Suicide Squeeze" was written by Jose Molina...which happens to also be the name of a baseball player who most recently played for the New York Yankees.
In "Wrapped Up in Death", Castle finds a familiar looking brown fedora and whip, donning the fedora as he examines a sarcophagus. The episode title itself sounds like yet another murder mystery/bestseller reference, this time to the "In Death" series by J.D. Robb.
Three Scooby-Doo references: Castle compared Beckett to Daphne and tells the villain "This is the part where you say 'And I would have gotten away with it too, if it weren't for You Meddling Kids!" and Beckett said the infamous "Ruh roh" towards the end of the episode after they find the killer.
When Castle mentions a gun that shoots ice bullets, he's bringing up a very old trope in murder mystery. Most recently, used in Deception Point, a Dan Brown novel that involves this (at least in the first act).
Both writer Jose Molina and actor Nathan Fillion, of course, are alums of Buffy (and, more importantly, Firefly). Allusions to these shows were frequent, especially in Season 2 when Molina was writing.
"A Deadly Affair" also shouts out to Breaking Bad - mentioned as "that cable show" about a high school chemistry teacher cooking meth, thought to be mirrored by the current case - and The Man with the Golden Gun, with Castle in the hall of mirrors in a pistol fight.
Castle gets to slip in a Double Rainbow reference while grilling Beckett over her lack of belief in psychics in "He's Dead, She's Dead".
"Anatomy of a Murder" has plenty of pretty blatant Shout Outs to Grey's Anatomy. It's also the title of a court drama movie starring Jimmy Stewart, considered one of the finest examples of the genre ever!
In "Famous Last Words," the murder victim led a band called Blue Pill.
"Almost Famous" features a completely made-up businessman named Mandelay, a reference to Seinfeld's fictional "Art Vandelay".
The same episode also contains a Jersey Shore reference where the names Sammy, Ronnie and Pauly are mentioned by a rather fake-tanned woman with a poof...
In "Nikki Heat" it is revealed that the Heat Wave screenplay was written by one Spike Rosenberg.
3XK features a killer that has returned to his original hunting ground and has a name involving three, like the Trinity Killer from Dexter.
Two suspects in "Countdown" are named Evan Bauer and Jack Cochran. In addition to the obvious reference, Robert Cochran and Evan Katz helped write, create, and produce the series.
"A Deadly Game" guest stars Mitch Pileggi as a spy involved in a secret conspiracy except he's actually just LARP-ing, and pulls out the old Skinner classic of throwing someone (i.e. Castle) against a wall to menace them into doing what he says.
In To Love and Die in LA, Castle and Beckett manage to recreate the "hesitating by the door" scene from Indiana Jones and the Temple of Doom. Which could be a coincidence, but the very next scene namecheck the Ark of the Covenant.
To Love and Die in LA also had an Open Sesame lock opened by taping the CEO's voice during a date, as seen in the movie Sneakers.
'A Song of Ice and Fire'' gets one when Castle mentioned that the victim being cut in half was "so Game Of Thrones".
In "Kick the Ballistics" the scene where Esposito distracts the bodyguard in the library is based on this scene from Beverly Hills Cop I.
In "Once Upon a Crime," they discover that the victims were being blackmailed over a car accident they caused years ago. Castle immediately references I Know What You Did Last Summer.
"Final Frontier", it is set at a sci-fi convention and cold-opens on the set of not-Star Trek/Firefly/Battlestar Galactica (which was cancelled after twelve episodes), ends with William Shatner's rendition of "Ideal Woman", and is filled with enough nerd allusions to upend a starship.
"A Slice Of Death" is one looooonnng homage to the noir genre. Even the episode's twist is a direct Shout-Out to The Usual Suspects. The murderer, a fan of noir, uses frequent references in their nefarious operations.
In the episode "Eye of the Beholder" there's a thief named Serena Kaye, a reference to Cat Woman aka Selina Kyle.
Sal, the epileptic hostage, is likely a reference to Dog Day Afternoon. Helps that he's the culprit.
The episode "An Embarrassment of Bitches" guest-stars Hilarie Burton, who played Peyton Sawyer in the show One Tree Hill. The episode title is probably a subtle reference to the aforementioned show, whose initial title was "An Unkindness of Ravens".
In "The Blue Butterfly", besides the general Noir style, Castle makes an explicit reference at the end, calling the titular Blue Butterfly "the stuff that dreams are made of". This also references the fact that the butterfly is a fake.
In "Once Upon a Crime", an episode about fairy tale-related crime, Beckett asks Esposito to look into a victim's bank account. He responds with, "As you wish".
Also takes place at a beach resort with a Chief Brady and a "shark attack" (really just a boat with a neon shark sign). And a lampshaded, "Not to get all Scooby, but he would have gotten away with it if not for you, Castle."
Within the first few minutes of The Final Frontier, Castle fires off 2 Firefly shoutouts: describing his excitement over a murder "shiny" and listing "that Joss Whedon show" as one of his favorite sci-fi series ever made. In addition, Firefly was cancelled after twelve episodes were aired while Nebula Nine was cancelled after eleven. Captain Max Renard sounds quite similar to Firefly's Captain Mal Reynolds, while Lieutenant Chloe rhymes with Zoe. And then there are the Creavers, the sworn enemy of the Nebula 9 crew, and the horrible things they would do to you (as Esposito describes to a disturbed Ryan) is like a g-rated version of what Reavers would do to you if they ever caught you.
The episode was directed by STNG alum Jonathan Frakes (who did a cameo) and featured Armin Shimerman (of both Buffy and Star Trek fame), and a variety of other sci fi references. Many behind-the-scenes production staff at Castle got their start with the original BSG or ST. Several recurring characters (Gates and Beckett's therapist, for example) were Star Trek regulars.
Despite several opportunities, the episode even manages to totally ignore Babylon 5, also a Star Trek tradition.
A pre-emptive Shout Out(or possible inadvertent spoiler); when learning about a murder at the convention, Castle asks, "What happened, Doc Ock finally caught up with Spider-Man?" The episode aired just over a month before the start of Superior Spider-Man.
At one point, Beckett suggests that Castle would look good as Doctor Manhattan: "Blue skin, brings out your eyes."
"Under The Influence" starts with a younger singer giving an older singer a Stealth Insult about her age, which was likely taken from Nashville.
"Scared to Death" brings a whole lot of contemporary horror movies into the fore, most notably The Ring. Castle and Beckett visit a suspect in a mental hospital in a scene reminiscent of Silence of the Lambs. Castle even calls Wes Craven for advice.
In "the Third Man", there is a close up shot of the "most eligible bachelors". The names of some of the writing staff have been placed under several of the photos.
The micro-Big Bad of "Taken" and "Hunt" is an ex-KGB agent turned wealthy industrialist named Volkoff.
In "The Human Factor" when reffering to two homeland security officers in black suit, sunglasses etc (who happen to be a black man and white man).
A general reference: the police officer characters are based out of the 12th Precinct of the NYPD. This was the same precinct that the 1970s police sitcom Barney Miller was set in.
In "Time Will Tell", Esposito mocks Castle's credulous reaction to the main suspect's claims that he's a time traveller by sarcastically suggesting that he was expecting the strange gadget the suspect was found with to be "Doctor Who's sonic screwdriver." He also suggests the suspect's story is derivative of Twelve Monkeys and The Terminator.
Also, when Simon disappears from lockup, Beckett asks where he is, Castle responds with "Not where, when." Which is a modified version of InspectorSpacetime's catchphrase. Not super overt, but Fillion himself guest-starred on Community.
In "Get A Clue", Castle puts a hand into a stone mouth and starts shouting. Might have been unintentional, but it might have been a Shout-Out to National Treasure: Book of Secrets, where Nicolas Cage's character does the same.
In "The Fifth Bullet", Castle suggests that the fifth bullet was an ice bullet. Esposito points out the bullet would still leave a bullet hole. Ryan corrects him by saying it would be an ice hole. Castle's response is "what did you call me?" All of which is a possible shout out to the famous "ice hole" Eskimo sketch in the American Whose Line Is It Anyway? series.
"Significant Others:" Having a character named Billy Piper is one thing, but having his wife be named "Leann" (Billie Piper's birth name,) stretches the believability of being a coincidence. Later Sonic Screwdriver references have confirmed there's at least one Whovian on the writing team, so the possibility of it being accidental seems even less likely.
"Smells Like Teen Spirit" is one big shout-out to Carrie, with a troubled, lonely outcast teenage girl being picked on by a gaggle of mean Alpha Bitches apparently discovering she has telekinetic abilities and seemingly using them to take revenge. Castle even mentions at one point that "Stephen" will love it when he tells him about this case. There are also some shout-outs to The Bling Ring when it turns out the Alpha Bitches are performing similar robberies.