* Gonzo starts helping Billy Bones pack when the latter says he needs to flee before pirates get him. The boys also fuss over the captain when he keels over in bed. ''Twice''.
* Mrs. Bluberidge gets a nice MamaBear moment when she tells the boys not to worry about her and to run to safety while holding off the pirates, in contrast to her usual bossy and overbearing personality.
* The scene where Kermit and Ms. Piggy sing "Love Led Us Here".
** The scenes intercutting Kermit and Miss Piggy's duet with Silver and the pirates finding the treasure are quite heartwarming, considering how many years they spent looking for it.
** The End Credits version is also very nice.
* While it's never [[ThoseTwoGuys really explored in-depth]], Jim's friendship with Rizzo and Gonzo does have some cute moments, such as when they affirm their TrueCompanions status at the Benbow, followed by a collective IWantSong.
** Later, when they join Capt. Smollett to rescue Jim, Smollett thanks them for joining him. Gonzo's simple response is, "Are you kidding? [[FamilyOfChoice Jim's family]]." And Rizzo firmly agrees.
* Silver and Jim's first conversation while stargazing. Silver apologizes for teasing Jim about his compass, and the two of them bond over having [[DisappearedDad lost their fathers]] at a young age.
* When Silver's crew turns on him:
--> '''Silver:''' Run, lad! Save yourself!\\
'''Jim:''' Why are you doing this for me?\\
'''Silver:''' Because I like you, boy. I hope you didn't think I was lying about that.
** And when Silver throws Jim's compass back to him before rowing away -- after refusing to kill him, no less.
--->'''Silver:''' Aw, hell, Jim. I could never harm you. You're honest and brave and true! ''(rueful grin)'' [[HeelRealization You didn't learn that from me.]]\\
'''Jim:''' [[MyFriendsAndZoidberg I learned it from my friends, Mr. Silver.]]
* Mr. Arrow lives! If for no other reason that this is the only ''Treasure Island'' adaptation where he lives. The fact that he's played by [[TheComicallySerious Sam the Eagle]] doesn't hurt either.
* Despite the fact that he's visibly straining with his eyes bugged out, Smollett won't let go of Benjamina after the rope on her DeathTrap snaps. As his rope gives out, Benjamina says, "Au revoir, mon capitan."
* What is Jim's first priority after Mr. Arrow scares the pirates off the ship? Save Captain Smollett. When he and his tiny crew see Benjamina trapped as well, he orders them to lower the ship's net to catch them. It almost works.
* Statler and Waldorf [[PetTheDog catch Benjamina and Captain Smollett]] when they fall from the DeathTrap. They claim it's because “it was too late to save the movie", but you know those curmudgeons care.
* The ship then ends up grounded due to Squire Trelawney overcorrecting. Smollett and Benjamina land on the sand, surrounded by pirates. Who leaps to action first? Mr. Arrow! He shouts, [[UndyingLoyalty "The Captain must have his sword,"]] swings onto the beach with two cutlasses, and fights through the pirate crew to toss a sword to Captain Smollett. He makes his way over to defend his captain. Captain Smollett comments happily that he's glad to see Mr. Arrow alive as they swing their blades.
* [[GoodAllAlong Sweetums]] turns out to be on the side of Jim and Cap. Smollett. He comes charging with a log as Captain Smollett shouts a warning to Mr. Arrow...and [[BigDamnHeroes knocks out the pirates that the two Muppets are fighting]]. Though it's got some elements of CMOF and CMOA to it as well.
-->'''Smollett:''' Wh-- Well, thank you, but aren't you supposed to be fighting ''against'' us?\\
'''Sweetums:''' Are you kidding? I love you guys! Ahaha!
* Every character coming to the defense of one another in the final battle against Long John Silver, which concludes with Silver being the epitome of a GracefulLoser.
-->'''Silver:''' Well, Mr. Hawkins, it seems your little family has come together against me. ''(hands his sword over to Jim)''