I have not seen anyone Riff a Supermarionation show such as Thunderbirds, Joe 90, Supercar, Nebula-75, etc. If I am wrong, someone please let me know, but would they work as a Riff?
KTMA did the Mysterons.
I’m moving this topic to “The Extended World of Riffing” since it’s about Rifftrax and not MST3K.
RiffTrax did the short Adventure in Telezonia as part of their Giant Spider Invasion live show. That’s the only marionette thing they’ve done that I can think of, but I’m probably forgetting something.
Attack of the Supermonsters has that vibe at least even though it’s more of an anime/live action models mashup.
Rifftrax did a short called Santa’s Spaceship which has an all marionette cast featuring the Bil Baird marionettes.
When it comes to laughing at the world of Supermarionation, it would be tough to best this classic bit from Dudley Moore and Peter Cook:
Well by Riff I meant make jokes about movies in the MST3K STYLE.