After Charley expresses disbelief at Throttle, Vinnie, and Modo being giant mice, Modo remarks "Were you expecting turtles, maybe?"
When Charley realizes Limburger's connection to the Plutarkians, she says "They're here" in the exact same inflection the phrase is said in Poltergeist.
In "The Masked Motorcyclist", the Biker Mice hear someone holler "Help" while listening to the radio. Vinnie remarks "Didn't know they did a Beatlestune."
Greasepit at one point refers to Charley as "Little Miss Annette Funicello" in "The Pits", who was one of the most popular Mouseketeers of the original The Mickey Mouse Club.
The episode "Steelfinger" features a parody of the James Bond franchise called James Bomb, the title itself being a play on Goldfinger.
"Steal of the Century" at one point has Vinnie exclaim "Takes a knocking and keeps on rocking", a play on the Timex watch's slogan of "Takes a licking and keeps on ticking".
"Back to Mars"
At one point, the Biker Mice make a reference to Superman by quoting the "faster than a speeding bullet" shtick.
The Sand Raiders' leader is named Slobber the Mutt, an obvious reference to Jabba the Hutt.
In "The Tribunal", Vinnie states that what he said as defense always worked on Perry Mouse-on.
"I, Greasepit" features a scene where Lawrence Limburger's profile is seen in silhouette while a snippet of "Funeral March of a Marionette" can be heard, a nod to Alfred Hitchcock Presents.
In "What Smells Worse than a Plutarkian Lawyer?", the manual the Biker Mice read to figure out how to shut down the nuclear reactor is written by a Mongomery Burns and on one page has a picture of Homer Simpson running with donuts in his arms. Vinnie even straight-up rips off Homer's "D'oh!" catchphrase as he sees the picture.
"Rocketh and Rideth":
When Limburger, Karbunkle, and Greasepit end up in the world of The Three Little Pigs at the end of the episode, they are dressed the way the pigs are depicted in the Disney short from 1933 and Greasepit quotes Porky Pig's catchphrase of stuttering "That's all, folks" before Limburger pulls him from behind the curtains.
In "Too Many Limburgers Spoil the Cheese", Vinnie quips to Greasepit that he can give his regards to Gilligan and Skipper after he knocks him into the sea.
2006 series
In "The Adventure Begins", Stoker at one point addresses Cataclysm as "Sylvester" and exclaims "Lucy, I'm home" before entering his hideout.
In "The British Invasion", Vinnie at one point addresses one of Sir Richard Brand-Something's robot minions as R2.
In "New Cats in Town", Vinnie makes a quip that the Catatonian shape-shifters' defeat is "like cats on a hot tin roof".
"A Hairy A-Bomb"
One of A-Bomb's mispronunciations of "Abominable Snowman" is "A-Whop-Doppa-Loopa-Doppa-Loom-Bam-Boom", a lyric from the Little Richard song "Tutti Frutti".
In "Bringing Up Vinnie", Vinnie quips "What's up, Doc" and Dr. Catorkian replies by saying to Vinnie "Oh, I see. You made a funny like a Bugs rabbit, yes".
The end of the episode features an homage to The Lone Ranger where Tanesha remarks "Who were those bikers?" and the Biker Mice parody the Lone Ranger's cry of "Hiyo, Silver!" before riding off.
"Surfer Cats of Saturn":
The Catatonian surfers Tane and Po'ele have a speech pattern similar to that of Yoda.