Curse the sudden, but inevitable commentary! Actually, don't do that, because we like to listen to commentaries. If you're like me, that is usually the thing you watch when you see something the second time around. And you can get all sorts of information and tidbits in these commentaries. I'll put a couple quotes from each commentary.
Summer Glau's introduction on the show, the shot revealing River in the cryogenic chamber is one of Whedon's "favorite shots...ever." He called it "visually stunning." Whedon recounts that shooting a scene in the nude is an awkward things to do, especially for a young actress on her first day. He also comments on Summer's first comments after coming out of the box... she asked if she looked fat.
The opening scene of Serenity was re-shot because it previously showed Mal in "the existential hell of a miserable person and why he wanted everybody to die and, apparently, that wasn't 'up' enough." Joss wanted to start the show with a bang and give the audience a scene that would allow us to see why Mal became the hardened "bad guy" he was.
Joss Whedon's never-ending self-depreciating humor is heard periodically throughout the commentary. He jokes that he was stoned when he got the idea for Firefly and that it's a bad idea to be that stoned. During the first scene with Wash, we see him sitting at the bridge playing with plastic dinosaurs. Whedon says "Obviously, very low budget dinosaur sequence. We just ran out of money and we wanted to have a world with dinosaurs in it, but just, we, you know, all we had was Alan."
Oh, yeah. And David Boreanaz is scared of chickens.
The Train Job
Joss Whedon (Executive Producer, Writer, and Director)
Tim Minear (Executive Producer and Writer)