Does a riff from the movie itself count? 
One of my favorites is the “It stinks!” (while making an okay sign) in Pod People, during the recording session.
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In Wild Rebels, when Rod is recruited by the police and they tell him they have a plan, Joel says “It’s called Operation Weaselsnitch.”
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“Spaz attack!” from the Undead when Satan’s minions are dancing around.
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Repeating “down, down” a la the professor guy in The Mole People. I just added it for my own enjoyment in The Killer Shrews. It’s quite versatile.
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Bill Corbett’s Crow could really get me laughing with straight-to-the-point riffs like “WHAT?”, “the hell’s this…” or even with a silent but dramatic head shake! I think it’s his tone of voice when he says them that does it.
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Bill’s Crow could have this very understated and very dry delivery at certain points, and those certain points were CLUTCH.
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Gee, you missed the ultimate mini-riff from Invasion of the Neptune Men: EAT IT, MOVIE!
and of course, “I’m HUGE!”
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There was nothing quite like a well-timed/well-delivered “Shut up, Iris.”
And I’m keen on a follow-up of another “Shut up” or “I tell ya, shut up”.
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“Do something!” from Manos. I’ve never related more with a riff than that.
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From Design for Dreaming, when the automated kitchen has produced a complete frosted cake with candles burning:
Mike: “I call no way!”
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Mitchell!
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It’s not even words; just the simple machinery-breaking noises they make when Cal’s assistant is stepping through the room with interociter parts in This Island Earth.
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mmmmManos.
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That reminds me of my favorite riff from that short.
“That squares my breasts!”
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i don’t really remember that, but i’ll be damned if i’m not going in asap. 
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Yeeeessss! The duck quacking bit is one of my faves. It’s just inexplicably funny to me.
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“You shove off!”- Red Zone Cuba
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Not a riff per se, but I crack up so hard any time Pearl says “Get bent.”
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