Characters frequently drink Pitt Cola. Given the similarity in the name and color of the can, this is a reference to Mr. Pibb soda. It was also named after Joe Pitt, one of the directors of the series.
Lazy Susan's name is a reference to the spinning table.
Pacifica Northwest's name is a pun on the U.S. region "Pacific Northwest," the region containing Oregon state.
Characters sometimes use a Tapeman, an allusion to the Walkman.
The book series " The Sibling Brothers" by Jenkins W. Jenkins, often read or referenced by Dipper, is a parody of the mystery novel series, published under the collective pseudonym The Hardy Boys Franklin W. Dixon.
When Dipper is exploring the cave, there are characters that look like runes. However, one of them does not match a known rune and the others do not translate into anything intelligible in English.
Mabel and Dipper walk past a taxidermy Jackalope in one scene.
For one frame, an image of Bigfoot flashes in the same pose as the alleged Bigfoot in the Patterson-Gimlin film.
Among the Polaroids are photos of Jackalopes, a Fiji mermaid, flying saucers, and the tabloid character Bat Boy.
Bill Cipher is a reference to the Eye of Providence.
In the ending, a photo with the logo on it is shown, and if one looks at the top right corner, two flying saucers can be seen in the same position as the two saucers over the Eiffel Tower in Paris in a famous fake photo.
The Konami Code is also visible.
In the animatic version of the theme song, Mabel and Dipper arrive on a "Fast Dog" bus. This is an allusion to Greyhound Lines buses.
The post card segment, near the end of the intro, shows a UFO to the top right. It is one of the Billy Meier UFOs.
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