- The Mystics chant in unison to call for Jen. True to their name, there is something mystical about it.
- The Skeksis Emperor spending his last seconds of life in holding on to his scepter when the Chamberlain tries to take it from him.
- The Trial by Stone, settling a long feud between the Chamberlain and the Garthim Master.
- Jen and Kira riding Landstriders.
- The Landstriders put up quite a fight against the dreaded Garthim, which were virtually unopposed up to this point. Even though they are ultimately outnumbered.
- Kira's Wing Pull, which saves her and Jen from falling off a cliff during a Garthim attack.
- The entire climax. Jen puts the shard back into the Crystal following Kira's Heroic Sacrifice. The castle is suddenly struck by light and openings are blasted everywhere to let the light in, making the Skeksis' dark interior fittings crumble and returning the castle to its original crystalline shapes. The Skeksis are hopelessly panicking, the Garthim fall apart into hollow shells and the zombified Podlings are returned to their normal state. The chanting Mystics enter the castle and gather around the restored Crystal, start emitting rays of light through their eyes that pull the Skeksis to them and stand up, and both species then merge into the single entities they were before the Crystal was broken, the UrSkeks.Aughra: What was sundered and undone / Shall be whole: the two made one!UrSkek: And now... the Prophecy... is fulfilled. We are again... one.
- Then the UrSkeks resurrect Kira.
- Brian Froud's amazing creature designs.
- It's an understatement to say that Jim Henson and his team turned TV and film puppetry into an art form. Many of the puppets (the Skeksis and Aughra especially) display very convincing emotions on their face.
- The entire movie's set design. Absolutely nothing in this movie is even remotely recognizable as an Earth-based organism. And it was all done with puppets - no CGI at all.
- The music score by Trevor Jones. Especially in the climax.