It’s always neat to see MST3K end up in the funnies!
There was the comic strip Gil Thorp, where we see an MST3K license plate.
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A few musical references:
First off, Lemon Demon, AKA Neil Cicierega, is a huge MSTie, and possibly the musical artist I’d most love to see write songs for the new series. He frequently references actors that have been in a lot of MST3K movies (like Robert Z’Dar) and most of his songs have that absurdist slightly mentally-unhinged quality so common in MST3K musical numbers.
His first album contained a cover of “Idiot Control Now”:
And his most recent album, Spirit Phone, contains a song called ‘Touch Tone Telephone’ (about a crazy UFO conspiracist calling in to the Art Bell show) which started out much differently about a certain movie familiar to many MST3K fans:
Dr. Frank of The Mr. T Experience references MST3K (along with a bunch of other geeky stuff) in his song ‘King Dork’
The band Headboard uses the phrase “How much Keeffe is in this song, Mikes O’Keeffe!” in one of their songs, Crank it Up.
The late great Logan Whitehurst was also a MSTie. I can’t think of any direct references offhand from his recorded stuff, but for anybody who knew him personally knows he was a fan, and he did sing a few bars of “He Tried to Kill me With a Forklift” once while playing a show in Davis, which is good enough for me. In other tangential relationships, “Every Country Has a Monster” got nominated for the Logan Whitehurst Memorial Award, and he did write a song about ‘At The Earth’s Core’ which posthumously got riffed on by MST3K:
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Almost forgot, The Laziest Men On Mars (who did the ‘All Your Base’ song) take their name from the line in Santa Claus Conquers the Martians
And nearly every song released by The Riverdales is based on a movie riffed on MST3K
especially their 2009 album “Invasion USA” which contains only one song that isn’t a direct MST3K reference.
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I guess Darkstar sorta kinda counts, eh?
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Tangentially, it also bears mentioning that well before Jonah Ray would become the new host of MST3K, he titled two of his comedy albums after MST3K moments inspired by Mystery Science Theater 3000: The Movie - “This is Crazy Mixed Up Plumbing” and “Hello, Mr. Magic Plane Person, Hello”.
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In an episode of Friday Night Lights, Landry’s new girlfriend says she’s hit the jackpot for their upcoming date night: a huge collection of MST3k shorts (and keep in mind this show was made several years after MST ended and before there was any word of bringing it back, so a reference like this was really out of nowhere). Sadly, she didn’t last long on the show. That girl’s a real keeper.
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In Wander Over Yonder, there is an episode called The Cartoon. The MST3K nod is fun as well as it being another great “making a cartoon”-type episode.
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I just saw this episode for the first time and wondered if it was an MST3K reference. Man, I love Craig McCracken cartoons.
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Superboy knows where to get pizza.
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LOVE that scene. 
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I’ve been binge watching Whose Line Is It Anyway and was shocked to see everyone dubbing over The Brain That Wouldn’t Die! Apparently they’ve dubbed over several things that were also riffed on the show!
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There was a show that predated Who’s Line? Called Quick Witz that had several members of the Who’s Line? cast, and they would also do the same sort of thing. They even overdubbed scenes from Eegah.
I specifically remember one of the jokes being where Eegah is talking and gesturing near a fire and the dubbers make Eegah out to be Jesus introducing Roxie to his Dad, God, as played by the fire.
It was much funnier than my explanation, I assure you.
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And another one. This one is from the award winning Adam Warren’s work Empowered (And for the record, there is only one way to describe Empowered. MST3K - Toobular Boobular - YouTube ).
And in case you think Mr. Warren is insulting us MiSTies, to be clear, this is a villain, at her most henious, dissing MST3K.
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Francesco Marciuliano has also used Sally Forth as a platform to express his fondness of Gamera.
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oh hey, shoutouts to neil cicierega! there was a song he did pre-lemon demon way back when he went by trapezoid and/or deporitaz (i’m not too familiar with the history of that, i only found out about it within the past 6-ish years, whereas this early stuff goes back to like the early 2000s)
… anyway it’s titled “No Respect For Pumas”
(fun fact: i heard this song before i ever actually saw the pumaman episode. it is decidedly a factor in why that line is one of my favorites. 
)
bonus round: neil c made some extremely audiovisual-sensory-stimuli-heavy works back in those early 00’s known as “animutations” (for real, don’t look into them if you have photosensitivity or audio sensitivity things. the humor in them is also very dated. very “thing that’s funny to a teenage internet nerd guy in the early 2000s”)
a lot of fans of those works also tried making their own, known as “fanimutations,” so it became kind of a little community. there’s a wiki and everything. and i don’t mean the wikipedia page for animutation (though there’s that too, and it’s very informative), there is an entire wiki resource dedicated to animutations & fanimutations.
backstory exposition aside, my point is this: the “watch out for snakes!” reference appears frequently in these works as a subliminal message. probably many other references too, but the snakes one is A Classic™
edit to add: i forgot to second the motion, agreed that it would be very very cool to see neil cicierega write songs for mst3k
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I’m not sure if any one here is into tabletop RPGs, but writer Christopher McGlothlin includes MST3K references in a lot of his works. He’s contributed to the Mutants & Masterminds RPG from Green Ronin, and almost always includes at least on MST3K shout-out, with the most notable ones being found in the Emerald City and Cosmic Handbook sourcebooks.
He also included some in his work for Deadlands: The Weird West, most notably getting one of the artists on board to have a picture of Dr. Forrester & TV’s Frank in the Dead Presidents adventure module. It ALMOST makes up for the rampant Confederate apologia. (Deadlands used to have it so their setting had the Union and Confederacy as two separate nations, with the Confederacy having decided to abolish slavery on their own. The publisher, Pinnacle Entertainment Group, has recently retconned that particular bit of awkwardness in the rebooted Deadlands: The Weird West.)
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The promising but short-lived Netflix show Everything Sucks! Set in the early 1990s. The nerdy young dude (and aspiring filmmaker) protagonist invites all his equally nerdy pals over to watch MST3K in an early episode. (I feel like the show might’ve held on longer with a better title.)
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I’m aware. I have my copy of the module signed by Trace and Frank. I was actually saving this one for another time when things got slow.
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