Although this was the original series pilot, introducing the characters and setting up their story arcs, it was the final episode broadcast in the show's original run on Fox.
After the Reavers are introduced, the screen goes to near black before cutting to commercials. Joss Whedon wanted to give the audience time to "breathe" before being hit with commercials, but a true black would automatically cue the ads. Instead, he went with a color that was as close to black as he could go without causing this.
The scene where Inara boards Serenity and is introduced to the passengers was initially filmed with Inara's original actress Rebecca Gayheart in the role, however Joss Whedon already felt that Gayheart wasn't right in the role (due to a lack of chemistry with the other actors). Having already decided to replace her, Whedon then shot the scene entirely as single-shots only focusing on a single character, therefore when Morena Baccarin was cast it was simply a case of filming her lines rather than reshooting the entire sequence.
In the pilot, during the opening sequence depicting the Serenity Valley battle, Captain Mal (Nathan Fillion) is seen using a DCA cannon. If you look closely at the head-up display interface of the gun, at the top center you'll see the Weyland-Yutani logo as seen on most of the Alien franchise movies. Alien Resurrection was written by Joss Whedon
For some reason, Jayne can be seen wearing an old-style German police jacket from the state of Rhineland-Palatinate.