Mulder compares his and Deep Throat’s relationship to the one between Luke Skywalker and Obi-Wan Kenobi. When Mulder gets angry once, he tells him to cut off the Obi-Wan Kenobi crap.
In "Small Pototoes", Amanda Nelligan is a huge fan who has seen the films countless times and is convinced that Luke Skywalker is the father of her baby girl. She hums the theme, and Scully asks whether Luke brought his light-sabre.
In "Vienen" after Doggett explains how five years ago, Mulder and Scully investigated the black oil substance that somehow curved into an alien colonization theory:
Mulder: And you’d like to help, but you left your light-sabre at home.
The guys on The Big Bang Theory are big sci-fi geeky nerds, and references the franchise quite often.
This strip edits Garfield's dialogue to be speaking in Yoda syntax.
This one does the same as the above, and also reverses the panels so it appears Garfield is using the force on Jon.
This strip contributes to the "I declare this house property of the X empire" Running Gag using the Galactic Empire.
This one edits a Garfield strip where Garfield declares he is absolutely not getting out of bed today, only for Jon to tell him there's a spider on his bed and him to jolt out immediately. His old response of "I keep forgetting we live in a generation without absolutes" is changed to "I keep forgetting only a sith deals in absolutes". As a bonus, the strip is titled "Don't Make Me Kill You".
After the initial sequence with Unicron the film's background is established with an Opening Scroll. (This is only in the British release of the film, because Britain was behind in the airings of the series. The American release jumped straight from the opening sequence to the credits.)
The movie's promotional material mentions that the film was "conceived in the epic tradition of Star Wars".
One of the film's primary characters, Arcee, has a head design styled in the likeness of Leia Organa Solo's famous "cinnamon bun" hair from A New Hope.
Megatron, at one point, uses a lightsaber type weapon against Optimus Prime. So does Hot Rod during his training.
The villain Unicron is a gigantic planet-destroying robotic spheroid, like the Death Star.
The sound effect produced when Rodimus Prime opens the Autobot Matrix is a combination of several lightsaber power-up sounds; Nelson Shin, who designed the sound, was also on the sound crew for Transformers: The Movie.
At the scene where Rodimus Prime receives the Matrix of leadership, the voice of Optimus Prime is heard. This is a reference to Obi-wan Kenobi saying the phrase "Use the Force, Luke" to Luke Skywalker in the Battle of Yavin.