- Many to MST3K
- Battlefield Earth:
Bill: Psssh. 3000. What has the year 3000 ever done for us?
- In the new Rifftrax intro movie, the Satellite of Love can be seen when the camera pans up into the sky.
- Revenge of Dr. X: "Looks like Tom Servo's older brother there."
- Battlefield Earth:
- The team also references Sailor Moon quite a bit.
- In 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.
- In Titanic (1997), 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 on the movie at all, as they hadn't riffed on many "good" movies yet.
- In the X-Men commentary, Bill "Crow" Corbett makes the "Can't we get beyond Thunderdome?" joke from Laserblast, to Mike's despair.
- On their commentary for The Dark Knight, Bill says, "Krankor?!", an allusion to a villain from Prince of Space, when the Joker enters and starts cackling.
- There's another Prince of Space riff in The Room. "I like you VERY MUCH."
- And yet another one in the Fantastic Four riff where Mike references the infamous "Your guns don't work against me!" lines, much to Kevin's amusement
- There's a scene in the X-Files movie near the beginning in which numerous 18-wheelers pull up, and Mary Jo says, Riding With Death 2: The Revenge of Robert Denby.
- Revenge of the Sith, when Anakin and Palpatine are sitting in front of the... bubble show.
- Star Wars 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 also has Mike commenting that General Grievous "needs a posture pal."
- In 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' which is a shout out to The Navy Lark, a common phrase said by the re-occuring Chinese villain.
- 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 Solo: Chewie, get us outta here!
Bill: Kalgan, take me away!
- Note also that "Calgon, take me away!" was the slogan used in Calgon bubble bath ads for years.
- The riff track for Star Wars: The Empire Strikes Back says that Tatooine went to hell when the Rakata were done with it.
- Star Wars: Return of the Jedi has Kevin (who was in MST3K as Tom Servo) shout "BRAIN GUY?" the during the scene where Luke is taken to Emperor Palpatine (Darth Sidious).
- A callback to "Time for go to bed" from The Unearthly in the Plan 9 from Outer Space RiffTrax nearly brought down the house at the live show.
- The RiffTrax Presents for Alien contains a tunnel sequence that is strikingly similar to the MST3K tunnel sequence. Bill prompts Kevin that it looks familiar, but Kevin is completely nonplussed.
- 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 beginning of the first X-Men movie has an establishing subtitle, "The not too distant future." Bill and Mike both comment on it.
- The Batman & Robin RiffTrax 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's riff is, "Guys, can he hear us?" Mike: "It could be worse, he used to be able to see us too!"
- 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 riff for 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 movies riffed on, 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 the riff of Harry Potter and the Chamber of Secrets, when Tom Riddle first appears, they make a reference to Tom Bombadil.
- Oceans 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 movie 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 Pareltongue, 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 The Last Airbender riff:
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 The Dark Knight riff at the end credits:
Kevin:"Oh, come on, what kind of crazy director would make his movie backwards?!?!?"
- 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 RiffTrax Live show for Manos: The Hands of Fate, 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 riff of The Dark Knight. At one point in the film, Kevin (speaking 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 the Rifftrax of Battlefield Earth, they comment that John Travolta's Evil Laugh makes Kang and Kodos, the space mutants from The Simpsons sound natural.
- In the live riff of Starship Troopers, 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:
- 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 The 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" from A Chorus Line during The Hunger Games.
- Teenage Mutant Ninja Turtles (2014):
Leonardo: "Back off, Raph."
Rifftrax: "Or you'll be diffusing 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)