* The ascension of Kida in the Crystal Chamber is probably the most memorable part of the movie, and generally the reason it's still recommended today. Any part with Kida as the Crystal is extremely impressive in animation, music, and mood.
* The entire opening, although watching Kida be forcibly separated from her mother due to the Heart may also count as a TearJerker.
* The submarine launch sequence. Particularly the sweeping CGI crane shot and [[CrowningMusicOfAwesome the accompanying fanfare.]]
* [[IronicEcho "Nothing.]] [[LastBreathBullet Personal."]]
* You gotta admit, forming a [[http://en.wikipedia.org/wiki/Atlantean_language fully functional language]] for this one movie is a pretty impressive feat.
** And hiring a linguist (the one who created ''Klingon'', no less) specifically for this purpose.
* The Crystal Chamber Scene for the gorgeous animation.
* Kida briefly fighting Rourke's men before getting overwhelmed. Even when she's apprehended, she doesn't submit defeat, she stares at her captors defiantly. Compare her DeathGlare with that of {{Disney/Tarzan}}.
* Milo [[WhatTheHellHero chewing out everyone who went along with Rourke's plan]].
* The Guardians of Atlantis being activated and shielding the city once more, this time from [[spoiler:the exploding volcano]].
* In the sequel. Carnaby's [[KarmicDeath demise]] at the mercy of the Dust Coyotes
--> '''Carnaby''': Uh, what is this?
--> '''Milo''': (angrily) Retribution.
* Also from the sequel, Kida riding the tentacles of the [[EldritchAbomination Kraken]] to rescue Audrey.