Adored by the Network: Cartoon Network was rather infamous for their annual 24-hour marathons of this movie in the early 2000s, which led to the movie gaining a cult following. The Hub quite likes to air it, too. Not to mention the guys who work on the other super-popular show state it was an influence on the friendship between the Autobots and the humans.
Supposedly the network adoration is mandated by Ted Turner himself, who saw the film for an in-flight movie and declared it one of the best films he'd ever seen.
Enforced Method Acting: Director Brad Bird made Eli Marienthal (the voice of Hogarth) run laps around the studio in order to sound realistically out-of-breath for one scene (he did this again later with Spencer Fox [the voice of Dash] in The Incredibles).
Real Life: The coordinates transmitted to the Nautilus are in Maine. The towns of Milbridge, Cherryfield, Harrington, Addison, and Jonesport are nearby, but the actual spot specified is a wooded area near the Atlantic coast.
Throw It In: The witness calling Agent Mansley "Mr. Manly" was actually a mistake by the actor, but they kept it in because it added to the gag of Mansley being a No Respect Guy.
Also, the movie itself was originally going to be a musical with songs by Pete Townshend, but the songs were dropped when Warner Bros. approached Brad Bird to direct the project.
There was originally going to be a brief flashback in which the audience would see a few vague details about the Giant's origins, but it was ultimately scrapped. The idea was to have a scene where he dreams about the alien factory where he was built, and to have the dream transmitted electronically to Dean's television for the audience to see. The scene was never animated, but some of the sketches for it can be seen here.