* The last two episodes. Everything about the message is perfect, it's like wrapping up the whole show in a ribbon, and it's what the whole show is about anyway; everything is connected, everything is magical. Learning Doc's name is a real highlight too.
** The same can be said for the final episode's special version of the closing theme, where many of the show's major characters (including the Fraggles, the Doozers, Marjory, Philo & Gunge, the Gorgs, Doc and Sprocket) all come together to sing the theme song.
** The final shot of the Fraggle Five dancing in Doc's new second floor apartment.
** The fact that Doc decides to move - because Ned, his best friend, has to move away for health reasons. Doc would rather relocate to stay with his friend than remain where he is.
** In the penultimate episode, we see the friendships between the Fraggles and Doozers and Gorgs that seemed impossible in the first season.
* In one episode, Doc and Sprocket are preparing for a blizzard. They see Ned Shimmelfinny's cat, Fluffinella, in the cold, unable to get home. So Sprocket, despite his dislike of cats and Fluffinella's fear of him, lets her stay with them until it cleared up, even sharing his doghouse. Fluffinella responds by cuddling against him and purring.
** That was the first season episode "Marooned", or [[TheOneWith "the one where Red and Boober are trapped in a cave"]]. That episode amounted to 22 solid minutes of heartwarming TearJerker.
* The song "We Are the Children of Tomorrow" gets everybody in the Rock to sing in unison, including Sprocket and Junior Gorg.
* In "Let the Water Run," one of Uncle Matt's postcards, he tells Gobo about rain. In the flashback sequence, as he's being drenched, a little girl comes over to shield him with her umbrella. He gives her a courteous "Thank you." Simply touching.
** Throughout the episode, Red keeps trying to do everything herself and refuses to accept any help. After Gobo reads Uncle Matt's postcard, she thinks she can restore the water by getting an umbrella. She tries to go to Doc's alone, but becomes too scared to enter the workshop. Then it turns out Gobo followed her.
--->'''Red:''' Gobo, I need your help.\\
'''Gobo:''' That's all I needed to hear.
* "Wembley's Egg" deserves some special mention, where Wembley befriends a Baby Tree Creature (Bird) and tries to take care of him.
* In "Pebble Pox Blues," when Wembley comes down with the titular sickness, Boober decides to forego his [[TerrifiedOfGerms germophobia]] to take care of him.