For the record, it's not funny in TotSM.

Right... It's a rather tense moment in the film, in fact. It's only funny as a reference.

Of course, I spent years watching Mystery Science Theater 3000, which is nothing but reference humor. Most of their jokes go over your head, but they fire so many at you that some of them are bound to stick. And out of the ones that do, the most obscure ones are the funniest, because it makes you feel like they're inside your head.