The entire opening, although watching Kida be forcibly separated from her mother due to the Heart may also count as a Tear Jerker.
When he opens the package from his grandfather and discovers it's the Shepherd's Journal, Milo's faith in his dream is reignited. Even when Mr. Whitmore (seemingly) discredits it as a fake, Milo firmly tells him he'd stake everything he owns that this is the real Shepherd's Journal.
The Leviathan attack scene is terrifyingly awesome. A Magitek 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.
Rourke's laconic reaction to Leviathan.
Rourke: Tell Cookie to melt the butter and bring out the bibs, I want this lobster served up on a silver platter!
After much trekking through the caverns (and a mishap with fireflies), Milo and the crew make it to Atlantis. And the panoramic view of the city is nothing short of breath-taking.
Rourke gets one a second later, when he shoots the knife out of her hand.
Milo showing backbone in the face of Rourke's demands sets him apart from the usual Hollywood Nerd:
Milo:(Off the crystal's description on the inscriptions) They're (The Atlanteans are) a part of it; it's a part of them. I - I'm doing the best I can here!
Rourke:(Unimpressed) Well do better.
Milo:(Getting sharp) Oh, I know. Why don't you translate, and I'll wave the gun around?!
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.
Heck, everything that Milo does during the climax.
Just Milo's character. Even before his Character Development during his journey, he stands apart from most Disney male protagonists as a cool nerd who believed in his passion, even when nobody else did. And after everything he's been through, he grows to be brave, dependable and honorable, even though the odds were against him.
The Guardians of Atlantis being activated and shielding the city once more, this time from the exploding volcano.
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 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.
Mole saving Audrey from falling by using his Tunnel King abilities to get to her. "You cannot live without me!" Audrey gives a huge smile for it.
After getting The Spear of Destiny, Kida takes out the two giants-by dropping Hellstrom's floating castle on top of them!
In the last scene, Queen Kida using the Spear of Destiny to raise Atlantis to the surface and Whitmore's voiceover assuring that things were much better for it. Also a Crowning Moment Of Heart Warming.