I suppose you could include Rifftrax if you want to, but I prefer the television series.
Anyway, my entry: The Screaming Skull Lady in haunted house hears knocks on the door. The knocks continue as lady listens and listens and listens…
“It’s Martin Luther. He’s nailing up each thesis one at a time.” 
What riffs would you consider more erudite than most?
Wow, I’m going to have to think about it, but that joke is not that smart or obscure. It will probably be a reference to an obscure TV show or old movie.
It’s a reference to Martin Luther, a 16th century priest and the father of protestantism. He wrote a letter to the pope codemning the sale of indulgences and which came to be known as the Ninety-Five Theses.
I remember one particularly unsavory looking character in a movie, and Crowe T. Robot said something to the effect that, “Wow, he makes Ignatius J. Reilly look dapper!” (or something like that). I don’t know too many people who’ve read A Confederacy of Dunces, so it struck me as pretty obscure, and quite funny.
The most obscure riffs would be the ones related to their own lives, like “She stole Mike’s keyboard!” They didn’t do too many of those, but there are some in-jokes nobody outside the show would get. The smartest one I can think of went like this:
Character in Hobgoblins: “Oh my God!”
Mike: “If that’s your god, you’re having a severe ontological crisis.”
I’m pretty sure Mahaloth was saying “the Reformation joke isn’t that smart or obscure. The smartest or most obscure joke will probably be a reference to an obscure TV show or old movie.”
Help me out here, Mahaloth.
That’s pretty obviously what he was saying.
Well, if that’s the case, I don’t see why that would necessarily be the case either. Having seen an old TV show that no one else has seen isn’t by itself sufficient to constitute a smart reference.
No, but the thread is also about obscure stuff.
Yeah. I mean, the Simpsons even has a Martin Luther joke in the Halloween episode where Lisa creates life. “I’ve created Lutherans!” IMHO, Luther and the theses are not exactly an obscure or particularly clever (although it’s certainly more clever than your usual jokes) reference, unless you were asleep during world history class in high school.
As for which MST3K references are really clever or obscure, I don’t know. There’s a lot of riffing that goes completely over my head.
There’s an episode riffing an old gangster movie with a title like “The Racket Girls” or some such that references, if I recall correctly, Minoqua, WI. Minoqua, WI is completely unremarkable except in that it’s a pleasant semi-touristy northwoods town with an excellent candy store and, well, my parents have a place up there.
That reminds me, I’ve heard at least one or two Tommy Barlett references in MST3K. Unless you’ve been to the Wisconsin Dells, or live somewhere where they’re heavily advertised, you’re not going to have a clue what the hell the guys are talking about. They do that quite a bit with Wisconsin/Midwestern references.
Yeah, I think local midwest references are going to be the most obscure. In The Creeping Terror they reference Minneapolis’s In the Heart of the Beast puppet theater. That’s pretty obscure.
Okay, but if their Martin Luther riff wasn’t world shakingly smart, can you guys come up with a smarter one?
I know.
You are right. I know about the reformation and so forth. I really must have been unclear.
Anyway, my point was that the most obscure would come from a tv reference like this:
In a movie featuring William Daniels, they riffed, “Michael, I want all copies of Captain Nice erased.”
It’s kind of hard to follow cause you had to know that he voiced the car on Knight Rider and that he made a failed 1 season show called Captain Nice.
See, the fact that I said, “*It will be *a reference to…” was supposed to indicate I was talking about what the obscure riff would come from or be about.
One particularity slow movie got “This thing has more pauses than a Pinter play!”
Nice. 
Hopefully, this won’t offend the OP, because I think it is a great idea for a thread, but… asking for “smartest” or “most obscure” riff are really two different things. Combining them into one thread is bound to be confusing.