I actually just realized that the film has a big reference to one of GL's favorite films (and mine), Forbidden Planet.
The basic plot of that film is that there was an ancient civilization on the planet of Altair 4 called the Krell. These beings had advanced knowledge and built a great underground city that had an unlimited power source, which when they hook their minds up to the energy gave them great psychic powers that allowed them to create with just a mere thought. The problem was that their subconscious created monsters from the "Id". The space ship in the film also looks conspicuously like the UFO that leaves Akator.
The idea that the "Inter-dimensional beings" had great psychic powers and that they helped create an ancient advanced civilization is a similar concept and an overt homage in my opinion. Also, the fact that Spalko gets the knowledge she seeks, but that it destroys her mind is also similar to the damage the Krell machine does to a weaker mind.
There are also references to Invasion of the Body Snathcers and Invaders from Mars in that those films used atomic fear and the fear that Communists would take control over our minds and "invade" the USA. Lastly I think that there's some inference to The Day the Earth Stood Still since that film was about aliens coming to Earth to warn about nuclear proliferation. I believe that the aliens and UFO left Akator at the end of the film as they knew that Earthings had gotten to the point that they'd use their knowledge for destruction (which is why having the atomic test earlier in the film was necessary).
Of course there are the musical references and other movie stuff, but I think these are the "meat & potatoes" of the film.