While filming the hovercraft chase scene, Joss Whedon told Nathan Fillion to "say something Mal would say." The result was the perfectly in-character line, "Faster! Faster! Faster would be better!"
Summer Glau had been pitching the idea that River would become a pilot while filming the TV show. She does so at the end of the movie.
Cast the Expert: A behind the scenes example. The camera man for River's second fight was a trained dancer, and was able to move around the scene to get the more dynamic shots.
Enforced Method Acting: Quite a few of Nathan Fillion's stunts involved a self-inflicted version. In his final fight scene against the Operative, he ended up slamming his face into the floor a few times; Joss was simultaneously impressed and horrified, and it took the makeup crew a moment to work out that he'd not only swollen his face, but also that he was somewhat dazed and struggling to read stuff in the background.
Fandom Nod: Adam Baldwin claims that Jayne's mini-gun was named 'Lux' after LuxLucre - the username of a fan called Kerry Pearson, who created fan art of Firefly and South Park. She died of diabetes.
Reality Subtext: In the flashback to Simon rescuing River, he says "she always did love to dance" - which is a nod to her actress Summer Glau being a trained ballerina.
Stillborn Franchise: sort of. The film did not recoup enough profits for a sequel, despite hopes that it would give new life to the Firefly franchise on film. That said, the books and comics followed.
Mal's angry rant after the opening heist and booting Simon and River off his ship was written at the last minute on the set by Joss Whedon when he realized that he needed to give a bit of additional context to the film and why Mal was so on edge. Nathan Fillion memorized the speech as the shot was being set up and the whole thing was completed in less than an hour after it had been written.
The scorpion kicks in River's fight scenes weren't a part of the original choreography. But when the fight coordinator saw how flexible Summer Glau was, he informed Joss Whedon who told him to add the kicks in wherever he could.
Inara's dress on Miranda was just a piece of fabric Whedon wrapped around Morena Baccarin and secured with a belt.
The Alliance soldiers lowering their weapons at the climax was actually the actors reacting to Whedon calling "cut". In post-production he kept the footage in.
Urban Legend of Zelda: It's been stated on various sites (including The Other Wiki) that the reason Book and Wash get killed off is because Alan Tudyk and Ron Glass were not interested in taking part in any sequels. Tudyk specifically stated at one con though, "I don't know about Ron, but that's not true for me! The reason I was killed off, is because Joss Whedonwanted me killed off!"
In the original script, Wash didn't die. None of the crew members did and in fact the film ended with Wash and Zoe promising to have children together.
Early storyboard sketches (some can be found in the Serenity companion book that has the shooting script) seem to show that River was going to be barefoot the entire movie. For example, she's seen barefoot in the storyboard for River's fight with the Reavers.. The novelization also seems to go along with this idea that River is barefoot throughout, as the narration mentions her being barefoot in the scene where they discover the dying Shepherd Book, even though she actually has boots on in that scene in the film.
The original blueprints to rebuild Serenity were lost at some point in pre-production. Nathan Fillion however had been so excited to be involved in the film he had taken pictures of every pre-production material he had seen - including the blueprints. This allowed the ship to be rebuilt as intended.
Write What You Know: the vocalist teaches history and geography outside of his music carreer, so he knows the subject.
General trivia
The pink symbol worn by Kaylee during the funeral was "double happiness"[1], which is a traditional Chinese wedding symbol.