Actor Allusion: When Milo first meets Commander Rourke, the latter comments that he "prefers a good western." This could be seen as a reference to James Garner's earlier television series Maverick, where he played a gambler in The Wild West.
Creator Killer: The film's failure at the box office stalled the careers of directors Kirk Wise and Gary Trousdale, who have since gone on to work on Dreamworks animated shorts.
Dedication: The movie is dedicated to Jim Varney who died from lung cancer partway through production.
Development Gag: The commentary tells a story about how there used to be a mystic named Zoltan (who used to speak in the third person, for some reason) along for the ride. At one point everybody sounds off after falling down a hole. For the longest time he was still there shouting "Zoltan is okay!" even after his character had been written out of the script.
Executive Meddling: The film was originally intended to be a creature feature adventure film. Then the Disney execs decided that they needed to get to Atlantis quicker, and so much potential was wasted. Kida was also downgraded into a Faux Action Girl due to this.
Genius Bonus: They did some research and then deliberately played with it.
Ichthyologists and paleontologists in the audience had to laugh at Whitmore's aquarium, which contained coelacanths (a 65-million-year-old species that was thought long extinct until its re-discovery in 1938.) Probably meant to show, in the most obscure possible way, that Whitmire's been exploring the world long enough to find all sorts of hidden things.
Cookie shows off a map on his belly showing "all 38 states." There were 38 states from 1876 to 1889 - the man's 26 years out of date. (Cookie's not all there.)
While abandoning the main characters in Atlantis, Rourke mutters, "P. T. Barnum was right." Mere gibberish unless you know Barnum's most famous (and probably apocryphal) saying, There's a sucker born every minute.
Recycled: The Series: A cartoon series called Team Atlantis was planned, but never came to fruition; the Direct-to-Video "sequel" is really just a few episodes of it strung together. Amongst the ideas proposed for this series was a crossover with Gargoyles, which is broady considered a canonical part of Gargoyles according to Word of God.
A crossover with Gargoyles was planned, but never made. Disney had been planning to make a series out of the movie, but turned it into a direct-to-video when it underperformed at the box office. This is also true with the future of this film's merchandise: To date, the only characters from the film that still appear in the merchandise are, due to Disney's merchandising policy of marketing the villains of flopped pictures, Rourke and Helga.
The submarine ride at Disneyland was originally going to be based off this film, but the film's failure resulted in that ride being based off Finding Nemo instead. However, there is a restaurant at Castaway Cay called Cookie's BBQ, and part of Port Discovery's background music at Tokyo Disney Sea is taken from this movie.
Jim Hill has an article that goes on in length about things that were cut from the movie, which includes deleted scenes of the Squid Bats and Lava Whales. There was also a plan, very early in production, for a magician character, Zoltan the Magnificent.
A behind-the-scenes footage found on the DVD release and one of the tie-in games shows the original intro was of a group of vikings searching for Atlantis only to be attacked by a sea monster while engulfed in a storm, fully animated, voiced and with sound effects. While mystifying, the executives felt no connection nor desire to learn more about the city or its inhabitants so the intro was done over.
Both end up Going Native and are "presumed dead" by the end of the movie.
In a broader sense, the Atlanteans have blue eyes, pale hair, and dark skin, just like Atlantean Thoth-Amon in Conan the Barbarian.
Several of the character designs look very similar to designs for characters with similar roles in Nadia: The Secret of Blue Water: Milo/Jean, Kida/Nadia, Helga/Elektra, Dr. Sweet/the Nautilus' doctor, and Santorini/the Nautilus' helmsman. However, the creators claim never to have seen Nadia: The Secret of Blue Water...