"The Pet" is pretty much a love letter to Alien. It takes place in a dark, enclosed spaceship. Sylvia dress up in an outfit that resembles Vasquez's (complete with face paint). The monster of the story is heavily Alien inspired with the fact that it spits acid and crawls around vents to kill people. At one point Sylvia rides around in an exosuit and quotes Ripley's famous line from Aliensalmost word for word.
There's also a blink-and-you'll-miss-it sequence of Captain Timnote the original Captain Tim, not the monster that Wander names after him doing a Captain Kirk-style speech.
And the Jump Scare at the very end of the closing credits is similar to one at the end of the Samurai Champloo episode "Cosmic Collisions".
In "The Hero", when Wander is singing Brad Starlight's theme song, Brad tells him to mention that he fought a bear so folks will know how strong he is. This is an obvious shoutout to Billy's theme song from Adventure Time.
The way Wander looks when he's giant and holding Sylvia in "The Void" reminds one of Attack on Titan.
What do you get if you stick Wander and Sylvia in Michael Crichton's sphere? You get "The Void." (No giant squid, but lots of jellyfish...)
In "The Birthday Boy", Wander's quest to throw an amazing party for Lord Hater—and get him to smile—reminds this troper of the episode "A Friend in Deed" from My Little Pony: Friendship Is Magic. It doesn't help that the Smile Song was sung in the MLP episode as well, and a similar song was sung by Wander (albeit his song didn't have the primary focus that Pinkie Pie's had—his was having a happy birthday overall; Pinkie's was all about smiling and not having anything to do about birthdays at all) in "The Birthday Boy".