For reference, the communication music is known as "Signals."
Listen carefully for musical Shout Outs to Jaws (when the mothership is communicating with the Devils Tower base) and Pinocchio (when Roy is being led into the ship).
The Special Edition of the main theme ends with a beautiful rendition of "When You Wish Upon A Star", which gets quieter and quieter, and at the end segues into a choir singing the five notes. One suspects John Williams wanted to sing the audience to sleep, and he did a good job of it.
The "voice" of the mothership was done by Jim Self, a legendary tuba player in his own right. Spielberg used him because the skill and difficulty of playing the tuba gave the mothership a "human" characteristic.
Everyone Is Jesus in Purgatory: The film can be interpreted as a metaphor for a spiritual awakening and journey: An ordinary man (Roy Neary) has an experience with a higher power (encounters UFOs one night on the highway) that completely changes his life (becomes obsessed with UFOs to the detriment of his family and social life) and is subsequently compelled by this higher power (through a mentally implanted image) to make a pilgrimage to a predetermined location (travels to Devil's Tower, Wyoming) where he communes with the higher power (takes part in First Contact with the aliens) and is ascended into the heavens (departs with the aliens after being chosen to join them). Roy getting sunburned by the UFOs during his initial encounter marks his symbolic baptism from normal everyman to alien contactee.
Six years after Close Encounters was released, Colorado suffered a real toxic-gas spill following a train crash that forced an emergency evacuation, much like the cover story that was used in the film to justify evacuating the Devil's Tower area.
An example for Steven Spielberg himself: he mentioned on an interview in 2005 that the fact Roy abandons his family to be taken by the aliens at the end isn't something he would have added to the script, if he'd had made the film nowadays, now that he is a father himself.
The humans who enter the mothership at the end are dressed in red jumpsuits and sunglasses, which in hindsight look like cheap versions of the aliens' outfits from the V1983 miniseries (in which the aliens did not turn out to be cuddly, friendly greys).
That little ball of red light that was always lagging behind the other alien craft, but is much too small to be another craft with a pilot inside flying it? Now we all know what that was all along; it was an alien drone that was being remote piloted by the other craft as a "rear lookout" or "rear guard" for the group.
Tonal Language: The aliens teach humanity a five tone greeting, essentially using a five letter word for greeting: H-E-L-L-O. During the "Dark Side of the Moon" scene, the aliens then try to give more "words," teaching the people present their language. Only problem: the only thing the people can say is "Hello" back. The aliens seem to get frustrated by completing the third "Hello" sequence like, "Yes, yes, 'hello', now let's try another word, Ok?"