!!First Movie
* 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.]]
* The Leviathan attack scene is ''terrifyingly'' awesome. A MagiTech monster big enough to be measured in ''miles'', a desperate battle for survival with torpedo-toting subpods and turrets, and finally a hair-raising, skin-of-the-teeth escape through a twisting underwater chasm.
** Of course, there's also Rourke's rather laconic reaction to seeing the Leviathan.
---> '''Rourke''': Tell Cookie to melt the butter and bring out the bibs, I want this lobster served up on a silver platter!
* [[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.
* On the subject of the Crystal Chamber, Milo showing backbone in the face of Rourke's demands sets him apart from the usual HollywoodNerd:
-->'''Milo''': (Off the crystal's description on the inscriptions) ...[The Atlanteans] are part of it; it's a part of them. I'm doing the best I can, here.
-->'''Rourke''': (Unimpressed) Well, do ''better.''
-->'''Milo''': (Getting sharp) Okay, tell you what. ''You'' translate, and ''I'll'' wave the gun around!
* 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]].
* Heck, ''everything'' that Milo does during the climax. Riding an ancient flying machine into battle against [[spoiler: Rourke's more ruthless crew]] to save [[spoiler: the crystal-infused]] Kiva, [[RammingAlwaysWorks driving said flying machine into the escaping balloon]] when all other attempts to stop it fail, and refusing to back down against Rourke himself [[NoHoldsBarredBeatdown despite being woefully outmatched.]] Bonus points for [[spoiler: using his wits (and a crystal-charged shard of glass) to ultimately beat his stronger opponent!]]
* The Guardians of Atlantis being activated and shielding the city once more, this time from [[spoiler:the exploding volcano]].
* CreepyAwesome: It's mentioned in the DVD commentary that after test screenings, the filmmakers asked kids what the scariest scene in the movie was. The answers were invariably either the climactic battle or [[MechanicalMonster the Leviathan]]. Kids were also asked what their ''favorite'' scene in the movie was... and the answers were invariably either the climactic battle or the Leviathan.
* CrowningMusicOfAwesome: The soundtrack is by ''James Newton Howard''. A special mention must go to [[http://www.youtube.com/watch?v=latiKSUzHho "The Crystal Chamber".]]

!!Sequel
* Carnaby's [[KarmicDeath demise]] at the mercy of the Dust Coyotes
--> '''Carnaby''': Uh, what is this?
--> '''Milo''': (angrily) Retribution.
* Kida riding the tentacles of the [[EldritchAbomination Kraken]] to rescue Audrey.