Although the Muppets have been the source of great joy and laughter, there have been some moments that have made viewers' eyes go into raw waterworks.
- "Time In A Bottle". Made even Harsher in Hindsight by the fact that Jim Henson is performing the character combined with the knowledge of what would eventually befall him.
- In the episode guest-starring Peter Sellers, things have been even crazier than normal in the theater, and Kermit's just about at the end of his rope when he has to go out and explain to the audience why the next act can't go on as planned. As he admits to being at a total loss, the curtains open on a bare stage...cue a particularly heartwrenching rendition of "Bein' Green", and grab the hankies.
- Gonzo's "My Way". Gonzo is preparing to leave the show for a film career in Bombay, India, and sings this as his farewell. It's so sad that even Gonzo breaks down and can't finish. Kermit has to interrupt the show to comfort him. Don't worry, he comes back.
- Harsher in Hindsight: With Jim Henson and Richard Hunt dead, Frank Oz retired, and Jerry Nelson retiring and then dying, Dave Goelz—Gonzo's performer—is the only one of the original five leads of The Muppet Show left. Rather than Gonzo leaving the people he cared about, the people Goelz cared about left him.
- The end of The Muppets Celebrate Jim Henson. The Muppets just discover this guy Jim for the first time and decide to put on a tribute show! But... this special was made in 1990. Just watch, and have tissues ready.
Fozzie: (reading a letter) "I feel very sorry that your best friend Jim died-" (the room goes quiet)
- Kermit, now puppeteered by Steve Whitmire, enters in the mist of their "Just One Person" tribute number. And photos of Kermit's previous puppeteer are seen in the background. Add to how, in this scene, Kermit is the only Muppet who already knew that their creator died, and even though he is nowhere near as sad as the others and mistakes their song as them finding the right performance for the special, he requests they "end it with something... silly." Perfect ending.
- So symbolic of how Jim Henson would be pleased to see Kermit being puppeteered and cheerful.
- On the same note, a special Sing! Sesame Street Remembers Joe Raposo and His Music was aired to honor the life and death of Joe Raposo - the special was taped in April 1990 and first aired on May 16. Jim Henson, who is interviewed in the special, died on the same day.
- During the middle of the special, Ray Charles' cover of "Bein' Green" (as featured on his album Renaissance) plays during a montage of behind-the-scenes moments with Jim Henson, including a clip from Sesame Street of him singing the song with a flock of Muppets. It ends with this picture◊ of Jim surrounded by his Muppets, that slowly zooms in on his face.
- Danny Kaye overhearing Statler and Waldorf talking about what a hack this weeks guest is, and telling Scooter "I think I need some cheering up." Thankfully, it turns into a Crowning Moment of Heartwarming when they realize they were mistaken about who the guest was this week, and tell Danny how much they love him.
- Watching the episode with Zero Mostel is quite a bittersweet experience, as he died before it aired.
- Gonzo's rendition of "Wishing Song" in the Madeline Kahn episode, when he realizes she's not in love with him.
- Roy Clark's almost eerily poignant version of signature hit "Yesterday, When I Was Young", complete with real (at least in the long shots) wistfully adoring pooch.
- The Closing Number for the Sylvester Stallone episode when he and the group of Muppets sings a tearjerker tale of "The Bird in the Gilded Cage." The song put everyone in the audience, including Statler and Waldorf, into tears.
- Say what you will about the heavily sentimental finale of the episode with Linda Ronstadt, but if you weren't trying to keep from vomiting, chances are you were trying hold back tears.
- In one ballroom segment, Gonzo is trying to find a dance partner, and keeps getting turned down by everyone he asks. In response, he sings a mournful rendition of "Won't Somebody Dance With Me". Fortunately, this turns into a Crowning Moment of Heartwarming when Camilla shows up.
- The show's re-imagining of Buffalo Springfield's "For What It's Worth" as an anti-hunting song... from the perspective of the innocent woodland critters being hunted, lead by a possum played by Jerry Nelson using his Gobo Fraggle voice. Chances are the three redneck hunters coming in between each verse being goofy were added to prevent viewers from curling up into a ball on the floor and crying.
These strangers come into our woodsWe'd understand them, if only we couldBut what's the reason they can giveFor not wanting you and me to live
- Then there's the way it ends with the animals staring at the viewer and whispering, in unison...