When Hermes sees that Leela is awake, he exclaims, "Sweet Three-toed Sloth of Ice Planet Hoth! She's awake!", referring to the ice planet from Star Wars Episode V: The Empire Strikes Back.
It is worth noting that this episode bears a great similarity to a season three episode of Stargate: Atlantis in which Elizabeth Weir falls into a coma and faces numerous in-dream delusions where her friends make numerous attempts to save her (as comparable to Fry telling Leela she needs to wake up). As well, both comas were caused by an enemy entity attacking the person infected (Dr. Weir, Niam. Leela, the baby Queen Bee.)
When Leela opens and falls into Fry's coffin, it is almost a shot for shot remake of the final scene in 2001: A Space Odyssey, when David Bowman gets absorbed into the monolith.
Hermes' comment about "Honeycomb's big, yeah yeah yeah," and the resulting response by Bender "it's not small?" (No no no) is a reference to an advertisement jingle from the 1980's for Honeycomb Cereal.
Furthermore, when the crew reaches the center of the honeycomb, Leela says "got it! The Honeycomb hideout!" This is a reference to the same 1980's ad jingle.
The episode's main plot of dreams within dreams would later be used as the central storyline of the movie: Inception.