The scene where Hoffman leaves the Gideon plant with Corbett and says "nobody made it" was filmed for, and edited out of, Saw IV (2007). Behind-the-scenes footage of this scene appears in Darren's Video Diary on the DVD and Blu-ray of Saw IV.
Understandably Scott Gordon-Patterson was a little apprehensive about sticking his head in a sealed box that would fill with water. The trap was tested beforehand and didn't go terribly well, which only added to his concern. Ultimately, the actor stepped up and did the scene himself without resorting to a stuntman. Several takes were required however to capture the scene as Patterson found himself uncomfortable at various points during the shooting of this scene.
The original screenplay called for the characters played by Meagan Good and Julie Benz to go through most of their ordeal wearing just their undergarments. The production team decided against this when they realized how committed and serious the two actresses were about their roles.
When director David Hackl screened the film for composer Charlie Clouser, the musician had to turn his back to the footage of the final ordeal for the last two contestants as he couldn't stomach what he was seeing.
The opening pendulum trap was a real working model. However, for the times when the actor was underneath it, the metal blade was replaced with a foam one. Likewise, the hand-crushers were foam too except for the close-up shots where they looked too fake. Real heavy duty material was used then with a prosthetic hand inserted.
This features one of the rare occasions when a crushing room actually crushes someone. Generally characters will manage to escape from such a scenario, for instance, in Star Wars: Episode IV - A New Hope (1977).