The sawed-off shotgun carried by Zoe throughout the series is the same prop gun that was carried by Lord Bowler on "The Adventures of Brisco County Jr." Submitted by Captain Defenestrator

The Alliance troops uniforms are the exact same ones used in "Starship Troopers" (mentioned on The Train Job commentary). Submitted by Cybermoose

The scene where Kaylee is in the engine room listening to Tracy's message again, on the work bench next to her hammock you can see a small figure of Han Solo frozen in carbonite from "Star Wars".

As Mal is bringing the shuttle in to land at the floating luxury home, as he flies to the left of a tower towards the gardens, behind them flying from right to left is the unmistakable silhouette of an SR-71 Blackbird cruising by. Given that this is a planet for the super rich and the heist is of a well known collector of old Earth artifacts, maybe this plane is part of another collector's collection, like John Travolta and his small fleet of planes including an airliner and other exotic aircraft.

When the crew returns from their raid of the Alliance hospital, Malcolm grabs Kaylee from behind and holds her in a friendly hug. This was improvised by Nathan Fillion, and was left in the shot because Joss Whedon felt it was such a natural movement for Malcolm to make. Submitted by Cubs Fan

Wash sets up a big red button for Mal to push to call back the shuttles if help arrives. He tells him "When your miracle gets here, just hit this button". After the show got cancelled, Alan Tudyk sent the button to Joss Whedon with the same message enclosed.