The 'Lion Sleeps Tonight' sketch, where the singing is actually keeping the titular lion awake, to the point where he chases the other animals off the stage. And onto Clifford.
In the Heather Locklear episode, Heather is hypnotized so that she switches from good to evil at the sound a double-clang. In the final number, Kermit keeps making that same noise with his cane. At one point, Heather begins hitting baby rabbits with her umbrella. Rizzo comments, "We're gonna hear from people."
The Andie MacDowell episode, particularly Bunsen coping with a mid-life crisis with the absence of Beaker, who is out on a Star Trek cruise bearing George Takei's constant egotistic talking. Then it ends on Takei and Beaker stranded in a frozen island. As Beaker finally teleports away, Takei moans how annoying Beaker was, until he continues his rambling to a nearby penguin.
Bunsen getting left with a sad and lonely man, figuratively and literaly, with the random appearance of Ben Stein in his cabinet.