- The planet Miranda in Serenity is a Shout-Out to William Shakespeare's Tempest and by extension, Huxley's Brave New World. Of course, this is also a reference to real-world naming conventions, as all the moons of Uranus are named after Shakespearean characters, and one moon is in fact named Miranda.
- River's Girl in a Box introduction is seen by many as a Shout-Out to the anime Outlaw Star.
- In the pilot, when the crybaby is released, Wash gives a shout out to The Beatles song of that name.
- In "Out of Gas", we learn that Serenity's first mechanic was a guy named "Bester." Later we hear Mal call him "Alfred." Alfred Bester was an important author in the post-war, founding era of modern sci-fi (as well as a character in Babylon 5).
- In a deleted scene from the pilot episode, Simon's encyclopedia can be heard mentioning a General Richard Wilkins who led the Alliance forces at the Battle of Serenity. Mayor Richard Wilkins was the Big Bad of season 3 of Buffy the Vampire Slayer, also created by Joss Whedon.
- "I was aiming for his head." - Avon says exactly the same line with regards to Travis in Blake's 7.
- A113 can be seen on top of the train in "Train Job".
- A subtle one to A Little Night Music. YoSaffBridge ran off with a security programmer named Heinrich who worked for her husband. At the end of A Little Night Music the main character's wife runs off with his son named Heinrick.
- The Weyland-Yutani logo is visible on the heads-up display of the anti-aircraft gun used by Mal in the pilot.
- Jayne's line "I was gonna get me an ear too" is very likely a Shout Out to Reservoir Dogs.
- One of the fictional historical figures is called Shan-Yu.
- Jubal Early's line "Well, here I am" could be a reference to the song "Space Oddity" by David Bowie: "For here am I, floating round my tin can "
- You might be aware that Joss Whedon is an avid reader of Henrik Ibsen. Mal being left naked in the middle of a desert is a Shout-Out to Peer Gynt, who ended up robbed and naked in the middle of the Sahara at one point in the play by a Bedouin girl who seemingly fell for his act.
- The cut down rifle Zoe usually carries is the same prop as the "Mare's Leg" from Wanted: Dead or Alive.
- In the opening of Shindig the Starlight Intruder from Dark Empire can be seen in the background.
Shout Out / Firefly