If I had to guess, I'd probably guess that it either a) came out of the MST3k writing room or b) came out of standup. Over the years, I've heard a few comedians say things like "Yeah, I do a riff on airline food in my act" and since most of the writers on MST3k also did standup at sometime, that's where I'd place my bets.
(And I'm pretty certain that the comedians borrowed the riff term from musicians.)