The Neverending Story is a Heideggerian fairy tale, where a young boy (through metanarrative) guides the protagonist Atreyu against the destructive force of The Nothing.
The most obvious Heideggerian strain is the use of negation to reaffirm life. According to Heidegger in "Being and Time" ("Sein und Zeit"), dread is the feeling of consciousness or existence (Dasein) rebelling against its negation. While The Neverending Story extrapolates this into a rather clichéd discussion on the slow dissolution of imagination, Heidegger would argue that the boundaries of negation are necessary for our understanding of where our selves end and where consciousness is bounded.
Still, this nothingness (and the concumbent anxiety) are adversaries to existence, and another Heideggerian theme can be seen in the need for active participation in the existence in order to preserve it. In his essay on technology, Heidegger posits that the most dangerous ideological trend is that of seeing other conscious beings as "standing reserve," or as merely materials of a use. Bastion finally sees the true existence of Atreyu and the others and is moved to react, yelling "Moonchild" (the name of the Child-Like Empress) out the window, thus conteracting The Nothing, the inevitable end of existence for what are posited as fully-functional consciousnesses.
Further explication of Heideggerian "nihilism" can be found in Sartré's "Being and Nothingness."