- Many to MST3K:
Kevin: Brain Guy?!
- Battlefield Earth:Bill: Psssh. 3000. What has the year 3000 ever done for us?
- In the new animated intro, the Satellite of Love can be seen when the camera pans up into the sky.
- The Revenge of Dr. X: "Looks like Tom Servo's older brother there."
- As a marquee for The Amazing Colossal Man appears in Attack of the Puppet People:Bill: Mike, bring up any fond memories? (Mike starts chuckling)
- Kevin notices something familiar about Palpatine when he goes to sit on his throne...
Bill: (chuckling) Who?
- Alien contains a tunnel sequence that is strikingly similar to the one in MST3K. Bill prompts Kevin that it looks familiar, but Kevin is completely nonplussed.
- Rogue One: The instant Bail Organa appears, Kevin gravely intones "Switch" — a nod to the series' long-running "Jimmy Smits" gag. Mike and Bill crack up.
- Bill finds the "the not too distant future" subtitle in X-Men familiar.
- The Dark Knight: When Harvey Dent calls Commissioner Gordon's plan "bold".Mike: Like barbecue sauce bold.
- Also on TDK, Bill says, "Krankor?!", an allusion to a villain from Prince of Space, when the Joker enters and starts cackling.
- Battlefield Earth:
- The team also reference Sailor Moon quite a bit.
- Dr. Who and the Daleks: The trio respond to a scene of two Daleks watching a video monitor by asking why anyone would want to watch a couple of robots watching a movie.
- Titanic: Kevin's line of "I'm gonna sink this bitch" for Captain Théoden is taken verbatim, at the exact same scene, from way back when Mike and the bots did a short special to look over the movies that were at the Oscars that year (one of which of course was Titanic). Notable for Bill saying in an interview that for the longest time, it was one of his favorite jokes in the history of the show.
- Reportedly, the chance to make this joke again is what prompted him and the team to riff the movie at all, as they hadn't riffed on many "good" movies yet.
- X-Men: Bill "Crow" Corbett makes the "Can't we get beyond Thunderdome?" joke from Laserblast, to Mike's despair.
- There's an early scene in The X-Files: Fight the Future in which numerous 18-wheelers pull up.Mary Jo: Riding With Death 2: The Revenge of Robert Denby.
- Star Wars:
- In The Phantom Menace, whilst continuing the Running Gag about certain aliens' notable Chinese accents one of them says (to a robot servant): 'Ahh, thank you, Number One', a common phrase by the recurring Chinese villain on The Navy Lark.
- Attack of the Clones has Mike saying "Into the Weenie-Mobile and off I go" as Anakin hops into a hovercar during the early assassin chase. It's a callback to the same remark in MST3K: The Movie.
- Revenge of the Sith, when Anakin and Palpatine are sitting in front of the... bubble show.Bill: So they're just going to sit alone in the theater seats and make wisecracks about the show? What jerks.
- Mike comments that General Grievous "needs a posture pal".
- When Darth Vader is slaughtering the members of the Trade Federation, one of the riffers shouts "Macken!!" during a close-up of a horrified look.
- A New Hope has a reference to the villain of Space Mutiny, one of MST3K's best episodes.Han: Chewie, get us outta here!
Bill: Calgon, take me away!
- Note also that "Calgon, take me away!" was the slogan used in Calgon bubble bath ads for years.
- The Empire Strikes Back says that Tatooine went to hell when the Rakata were done with it.
- A callback to "Time for go to bed" from The Unearthly in the Plan 9 from Outer Space live show nearly brought down the house.
- A similar thing happened during their holiday shorts-stravaganza, when a man popped up dressed in a space costume: "Santa's new assistant, Prince of Space!"
- The Batman & Robin riff features Bill mentioning on Woodrue's "lifelong dream to shoot a man into space and force him to watch really bad movies!"
- Also, when Ahnold says, "I hate it when people talk during the movie!"Bill: Guys, can he hear us?
Mike: It could be worse, he used to be able to see us too!
- Also, when Ahnold says, "I hate it when people talk during the movie!"
- In D-War, concerning the Atrox Leader's absurdly deep voice: "Rowsdower? Is that you?"
- Kevin says "NO SPRINGS! (beep boop)" after a bicycle crash in the safety film short "One Got Fat". The line and sound are taken from the educational short A Case of Spring Fever.
- In The Lord of the Rings: The Two Towers, there's a callback to the MST3K running gag "SLEEEP!".
- In Planet of the Dinosaurs, there are some mentions of other planet-themed riffs, such as The Phantom Planet and Women of the Prehistoric Planet. Plus references to the "Roll Fizzlebeef" name list from Space Mutiny. And a shoutout to The Mighty Boosh.
- In Harry Potter and the Chamber of Secrets, when Tom Riddle first appears, they make a reference to Tom Bombadil.
- Ocean's Eleven:Rueben Tishkoff: I know more about casino security than any man alive. I invented it, and it cannot be beaten.
RiffTrax: It's like Battletoads.
- Kevin says that Casablanca is the first of a trilogy, the last of which is Overdrawn at the Memory Bank. Bill thinks it sounds familiar.
- "Okay, so when they chop the big bad guy's hand off, his blood started smoking and then turned into giant scorpions. Are we sure this isn't an episode of Axe Cop?"
- Lots of Monty Python quotes. Seems to work pretty well for riffs.
- "What, you think the guy in the $3000 suit is gonna be rowing an oar? Come on!" (The guys directly shout out A.D. a few minutes later, saying they miss it.)
- They also reference Arrested Development during The Room whenever the infamous chicken impressions start up.
- In Harry Potter and the Chamber of Secrets's riff when Harry speaks Parseltongue, we get, "Which of course is snake for 'Watch out for snakes!'"
- A surprisingly obscure one from the "Drawing Rectangles" short, when the narrator is drawing a radio: "To the left of the dial, draw The Replacements."
- Later in the same segment, when the "artist" adds the knobs: "Knobs may be eaten by Karl Pilkington, but only at night."
- Back-to-back ones from "Don't Be a Bloody Idiot": "Torgo's got a gun!" and "How not to be seen".
- From The Last Airbender:Yue: "It is time we show the Fire Nation that we believe in our beliefs as much as they believe in theirs."
Kevin: "I don't believe that you believe in your beliefs. Believe it!"
- In The Dark Knight, at the end credits:
- A scene with Jacob in Breaking Dawn has Bill saying "Sleeping nose to anus is something I'll never get used to," then quietly whispers "wahrwilf."
- In the Manos live, the riffing begins with Kevin saying "Wow, this really looks familiar...". He then says that it's video from his "vacation in hell".Mike: Actually, Kevin, this looks like El Paso.
Kevin: Like I said, hell.
- They like to reference Lost quite a bit, particularly their disappointment with the last few seasons. A very subtle reference was made during The Dark Knight. At one point, Kevin (as the mayor of Gotham City) says "Get off the island, you say?" The mayor was played by Nestor Carbonell, who also played Richard Alpert on Lost.
- In Battlefield Earth, they comment that John Travolta's Evil Laugh makes Kang and Kodos sound natural.
- Buffalo Rider references Battlefield Earth, Friday the 13th, Keeping Up with the Kardashians, Sam Elliott, Rashida Jones in Parks and Recreation, and Mark Ruffalo in The Avengers, Collateral, Date Night and Zodiac.
- The Devil's Hand references The Adventures of Milo and Otis, Batman, The Beatles, Bonnie Tyler, "Total Eclipse of the Heart", Clint Howard, Gary Wright, "Dream Weaver", John Ashcroft and Tara Reid.
- In the Starship Troopers live, when the ships are deploying for the final battle:Mike: And Slippy Toad was shot down immediately.
Kevin: Well, Zim was always good at invading.
- At the end, when all of the glory of winning the climactic battle is given to Sgt. Zim:
- Treasure of the Amazon:RiffTrax: We've heard tales of your cruelty. The Birdemic is nigh.
- Zindy, the Swamp-Boy:RiffTrax: What's in ze bag, a shark or something?
- When two characters in Attack of the Puppet People are seen watching The Amazing Colossal Man, Kevin and Bill ask Mike if it reminds him of anything. This also works as a shout out to the MST3K riff of Gamera (from the same season as Amazing Colossal Man), where the bots asked the same thing to Joel when a rocket ship is shown taking off.
- The riffers briefly sing "I Hope I Get It" during The Hunger Games.
- Teenage Mutant Ninja Turtles (2014):Fitness Guru: Twenty years Ive studied the animal kingdom. There are fat pigs, fat cows there are no fat birds.
RiffTrax: Uh, what about ostriches, penguins, that red Angry Bird?
Raphael: See, she's looking at us like we're freaks. I bet that's why you took our picture, wasn't it?
RiffTrax: Say, you're pretty sharp for a Battletoad.
Leonardo: "Back off, Raph."
RiffTrax: Or you'll be defusing all the bombs in the underwater level.
- Transformers: Revenge of the Fallen:Optimus Prime: "We've witnessed your human capacity for war."
RiffTrax: "We know what it is good for." (referencing Edwin Starr, War)
- In Supersonic Man, Kevin recognizes the name Cameron Mitchell as "Captain Santa" from Space Mutiny. Bill voices his displeasure at his character's base having loads of railings, remembering the film's various Railing Kills.
- Disembaudio is often depicted as a toaster eerily similar to The Brave Little Toaster.
Shout Out / RiffTrax