* The entire [[GoodTimesMontage montage]] of Jim's growth and the development of his friendship with Long John Silver, inter cut with flashbacks of his father abandoning him to show Silver as his [[ParentalSubstitute father figure]]. Also set to the lovely [[CrowningMusicOfAwesome I'm Still Here]] by John Rzeznik.
* The ending: Although these days it's practically required by ''Literature/TreasureIsland'' remakes to turn Silver into a surrogate father to Jim Hawkins, this movie did it in a warm fuzzy believable way that gets you everytime.
* "Now you listen to me, James Hawkins. You've got the makings of greatness in ya, but ya gotta take the helm and chart your own course. Stick to it, no matter the squalls! And when the time comes, you get the chance to really test the cut of your sails, and show what you're made of! ...Well, I hope I'm there, catchin' some of the light comin' off ya that day..."
** And he was. (In a BeCarefulWhatYouWishFor kind of way.)
** And the soundtrack accompanying the scene? [[https://www.youtube.com/watch?v=Gd8W9ibw4Es "Silver Comforts Jim"]].
** Silver (After Jim saves them all): "DIDN'T I SAY THE LAD HAD GREATNESS IN 'IM!?"
** When Silver is leaving, he asks Jim if he wants to come with him. Jim replies that his old self would have jumped at the opportunity, but thanks to Silver's encouraging words from before, he's going to create his own path instead. Silver remarks that Jim is glowing "like a solar fire", like he knew he someday would. The two share a tearful goodbye hug, that Silver initiates no less.
* And for the cherry on the icing on the cake, "Always Know Where You Are" playing over the credits.
* [[spoiler: Silver sacrificing the treasure in order to save Jim. And then as he's leaving, he tosses some treasure from his pocket (which was most likely the only treasure he managed to get) so Sarah could rebuild the Benbow Inn]].
** Considering, Silver was the one (along with the other pirates) who burned it down, this is kind of a roundabout way for Silver to make up for his past misdeed. The fact that he specifically says the gold is for the inn practically confirms it.
* Two things in particular: At the end, Jim looking up at the sky and seeing a cloud-form Silver smiling down (complete with a star for [[ElectronicEyes his eye]]), and this quote:
-->'''Silver:''' Look at you! Glowing like a solar fire. You're something special, Jim. You're gonna rattle the stars, you are!
* Doppler and Amelia's growing, if subtle, relationship throughout the movie:
** The moment after [[spoiler:escaping Treasure Planet's destruction via a portal back to the Spaceport]], Doppler and Amelia hug in joy... then after a few seconds, they look at each other... and smile. D'awww.
** A few scenes later we find out that [[spoiler:they are HappilyMarried with four kids: Three girls who look like their mom and one boy who's the carbon copy of his father]].
** Amelia: "Doctor... you have wonderful eyes".
* A little moment during the supernova scene, as they ride the last wave out of the dying star: Jim is pressed against the mast and his lifeline, scared to death, and Silver has both his cyborg arm and his whole body around Jim, protecting him from whatever goes flying after them. And Jim, the boy who plays with danger all alone, doesn't even realize he has someone protecting him until they're safe and he opens his eyes.
* [[AdultFear "Jim, I don't want to lose you!"]] "Mom... you won't. I'll make you proud."
* The scenes where Silver [[PetTheDog dotes on Morph]] are quite adorable.
* ''Beware of spoilers.'' [[http://theflyingredpig.tumblr.com/post/53225717071/crispy-ghee-crispy-ghee-though-being-active Reunited.]]