To clarify, I’m referring here to running gags that for the most part were limited to the episode they originated in, not the ones that went on to turn up sporadically forever after.
(No “Hai Keeba!” or “I sing whenever I sing whenever I sing” etc)
One of my personal favorite batch appears in Season 7’s NIGHT OF THE BLOOD BEAST where Mike and the Bots act as if the Blood Beast is a newlywed meeting hostile in-laws.
(That episode also has some good ones with the apparent cheapness of NASA, the perceived confusion over who is named what and how easily distractible everyone seems.)
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The Jay Ward homage in Fugitive Alien in which Crow keeps yelling “AGAIN?!” anytime someone onscreen calls out to Rocky. Joel’s escalating irritation with him is just the icing on the cake.
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Also, the constant reminders of poor old bean-eating dad in High School Big Shot.
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They didn’t do it throughout the episode, maybe pulled it out 3 or 4 times, but the “took the pipe” gag in Devil Doll kills me. And the funny thing is, that’s the first time I ever heard that phrase, so it wasn’t one of those knowing, esoteric things - it’s just sounded funny (the line and the way they said it) - “Boy, did we take the pipe” 
Also, for Rifftrax, the Creedence stuff in Copper Mountain was a hoot.
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If we’re talking later MST3K, the spate of recurring gags about the missed lunch date in Avalanche is pretty funny.
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Would you forget the skid marks!!
And the knee-up jokes.
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“It’s Manos: The Hands of Fate…” “Manos: The Hands of Fate…” “Manos…” “The Hands of Fate?” The repeating of the experiment’s name in Episode 424 takes the cake for me. It’s one of my favorites. It makes it special. The name as a catch-all for all of the movie’s sins.
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I really liked the “TORTUUURE” gag from Teenagers from Outer Space
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“Liar! Liar!” from I Accuse My Parents
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I just finished “Danger!! Death Ray” and got a big kick out of their riffing whenever there was a specific musical cue. They rag on the main theme, but the one that made me laugh the most was when there was a cut to a new shot and a tympani kick and one of them would say “This man will compete …!”
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“Pizza Pizza…” in Hercules Against The Moon Men (1966). “Pizza, Pizza, Pizza, Pizza…” This running gag made me fall in love with the Little Ceasars slogan. Whenever I spy a Roman soldier in something today, “Pizza Pizza” pops in my mind.
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Warrior of the Lost World and its not knowing how to spell “perimeter.” What really makes it beautiful is that the last time, Crow just silently shakes his head.
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Let’s not forget the running gag of them doing the parrot whistle every time the Blood Beast shows up late in the episode. Cracks me up every time!
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The Thing That Couldn’t Die has several
The Jessica song kills me. Especially when Flavia calls out her name repeatedly and each time Tom starts the tune a new.
The “you’re all evil” bits
Repeating variations on Flavia’s way of pronouncing “TRAY-sure”
Singing variations of “Oh, what a beautiful morning” (“There’s a bright yellow stain on my back brace!” etc, etc)
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Cave Dwellers (1984) held four I directly think of. “Ends of the Earth… Ends of the Earth…” “Ends… of the… Earth…” If I eye people traveling great distances onscreen, “Ends of the Earth” isn’t that far away. Second? “Dong?” “No it is Thong isn’t it?” That byplay of saying “Dong” followed by “Thong” screams Cave Dwellers and 301 made it shine. Third? “Comic book…” “No it’s a Graphic Novel…” The innocent utterance of “comic book” run down by the quick correction made me smile every time. Fourth? This one has some runoff in later episodes yet the bulk and legacy of the riff remains here. “Stately Wayne Manor…” That joke so fits that experiment as a backhanded comment on the cheapness of the production.
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The reoccurring riffing on the actual ages of the alleged teenagers in I Was A Teenage Werewolf were hysterical.
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Probably the song riffs in Werewolf.
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Has everyone in this thread signed Sherry’s birthday card?
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