When the aliens are investigating the junk in the basement, one of them plays with a bicycle wheel. This is a reference to the original book; the main character observes that, with all the advanced technology the aliens possess, they do not use any wheels, and wonders if the alien life form had skipped the invention of the wheel.
One scene shows Ray running out of the house to find Robbie while dozens of people are right outside his house photographing the lightning storm. To film the scene, producers hired people on the street to come to the street at the time of shooting with a camera and film so they could get pictures of Tom Cruise for free.
During the filming of the underwater scenes (where the ferry capsizes), director Steven Spielberg played a prank on Tom Cruise and Dakota Fanning by playing the dramatic music from Jaws (1975) (also one of Spielberg's films) through the massive underwater speakers on the sound stage.
While filming nearby, Tom Cruise, along with a twenty-member entourage including Steven Spielberg, visited a Lexington, Virginia Dairy Queen. Cruise saw a jar on the counter with a photo of Ashley Flint and her story. Flint had been in a go-cart accident a few months earlier, leaving her family with a mountain of hospital bills. Cruise put $5,000 cash into the jar.
Ray's horror at discovering ash all over himself after stumbling home was influenced by September 11 survivor stories.
Gene Barry, Ann Robinson: the grandparents appeared in "The War of the Worlds (1953)" as Doctors Clayton Forrester and Sylvia Van Buren. This was Barry's final film.
Steven Spielberg: [fathers] The main character is a divorced father whose children are angry at him, mirroring Spielberg's experience with his absentee father.
Steven Spielberg: John Williams scores. A short sequence of notes, repeated used as a signal to the audience. The tripods use a long, drawn out, low tone (like a foghorn), followed by a higher pitch (sounding like an orchestra), as a way of communicating to other tripods (as it was in the book). The two notes are similar to the two notes used in Jaws (1975). As in different attacks in the movie, like the beginning of the Hudson Ferry attack, it announces to the audience that something is about to happen (again, like in Jaws (1975)). In that scene, it seems to mean "Come here, other tripods, I've found a bunch of humans." As a counter-example, though, the same tones are used at the end of the "aliens in the basement" scene, and seem to mean a rallying signal, as in "everyone, report back to your posts", as the aliens immediately leave. Note, also, that a basic five-tone sequence was used in Close Encounters of the Third Kind (1977), as a connection to that film's aliens.
Steven Spielberg: [Signs] Using a sign with directions or instructions as a joke. In this case, as the first buried machine is tearing up the street in Ray's hometown, causing all sorts of damage, the camera pans past a close-up of a municipal "No Littering" sign.