The director of MIST is nicknamed Hal, whilst the are scientists named Bowman, Poole, Floyd and Chandra. These are references to the movie/novel 2001: A Space Odyssey and its sequel, 2010.
When you're in a small town somewhere in the Mojave desert, still on CD #1, in one of the stores you can see a pinball with an Einhander (aka Einhänder) theme, although Aya doesn't get a chance to play it. An obvious easter egg showing yet another SquareSoft game.
The Parasite Eve series was based on a Japanese horror novel by the same name, written by Hideaki Sena.