When Homer and Mr Nakamura get drunk on snake wine, the visions they see are based on elements from the films of Hayao Miyazaki (My Neighbor Totoro (1988), Spirited Away (2001), Howl's Moving Castle (2004), Kiki's Delivery Service (1989)).
After Milhouse expresses a wish that someone would have come from the future, and warned him not to talk to Harlan Ellison, Ellison accuses Milhouse of stealing his idea. This is a reference to Ellison's allegation that The Terminator (1984) was based on his script for Soldier (1964).
Stan Lee has a cameo, during which he says "I can only watch, I cannot interfere." This could be a reference to the theory that during Stan Lee's cameos in all the Marvel movies, he is actually the character Uatu, The Watcher.
The Atomic Discombobulator under the desk in Comic Book Guy's shop was previously seen in 'Homer's Phobia'.