The twist at the end was definitely cool, but after the adrenaline wore off, logic tried to reassert itself. How did John stay so still? How did they not hear him breathing? When you rewatch the film, it gives you the answers: presumably he took the same nerve agent that kept the man from whom Amanda had to retrieve the key to her trap immobile, and his breath would naturally be rather weak given that he had cancer.
The flashback to the Bathroom being set up from Saw III confirms this.
Why, of all places, is the very first trap to appear in the franchise set in a bathroom? Because Jigsaw wanted to be there in person, posing as the "corpse", and he knew the lack of decomposing-body odor would eventually tip off his captives if the room didn't already reek of stagnant bathwater and backed-up toilets.
There's also the fact that he was facing away from Lawrence while his face was in Adam's view. There's no doubt that he did it to avoid Lawrence from recognizing him as one of his patients.
It has always been unclear to me why Lawrence's wife and daughter were also a part of the test, when they weren't shown to do anything even remotely bad. I think now that John knew Zep wouldn't kill them. Zep did have a sadistic streak and enjoyed the power he suddenly had, waving the gun around and making and smug comments to the video feed from Bathroom Trap. On the other hand, he was quite clearly a coward (and scared shitless when he suddenly had to fight Tapp, or even when Lawrence discovered his identity), and as John knew him before, presumably he knew Zep wouldn't be able to murder a defenseless woman and girl in cold blood even under death threat. Especially since it seems that his primary goal was to kill Lawrence rather than them. Of course that assumes that John could predict all that, but you pretty much have to accept that he's omniscient to take these movies seriously anyway.
Another possibility: Zep was never supposed to kill Lawrence's wife and daughter in the first place, just Lawrence himself. That explains his gun-waving nicely; he had only to scare them (to put pressure on Lawrence), and did exactly that (in a clumsy manner fully expected from someone who doesn't do this sort of thing on a regular basis.) Notice how when the time runs out he doesn't tell them "I'll kill you now", he says "Lawrence made a mistake and I'll do what I have to do." Alison's sudden attack and Tapp's intervention prevented him from executing his original plan, but notice also when he stuns Tapp with a vase for some seconds, he doesn't go after her; rather, he declares, "Now I'll kill your husband" and goes off to do exactly that. The only thing that contradicts this theory is Zep's tape, which says "Will you murder a mother and her child to save yourself?" However Adam didn't play that tape to the end; maybe the actual rules clarified that he needed only to threaten them with murder. A weak point, I know, but it makes everything else much more understandable.
Zep didn't chase them because by that time he probably wouldn't find them before they had alerted somebody, and Word of God is his gun-waving was because he was enjoying finally having control over somebody else. And Adam did play the tape to the end. Jigsaw is simply a liar, a hyprocrite and a Manipulative Bastard and narcissistic sociopath- most of his victims are people he already knew who either annoyed him or whom he was envious of; his philosophy is not meant to be taken seriously. Given the amount of planning that goes into his traps and schemes its more likely that he is just a power-control serial torture-killer who feels the need to have people appreciate him 'vis a vie'' "saving" them and converting them to his cause, and he is perfectly willing to kill innocent people to do it (since he is never the one who actually pulls the trigger, he can probably make excuses for himself). He may be narcissistic enough to believe his own lies, but in the end he is just a loser (in his own mind) who wants to feel important.
It ultimately turned out that Lawrence wasn't lying, at the end, about bringing someone back to Adam at the bathroom. It just took him six more movies to do it, and by the time he brought Hoffman there, Adam was roughly-a-year-or-so dead.
Mark Wilson is put in trap that's near impossible to escape from... all because he liked to fake being sick to get a day off the work. This might seem to be a Karmic Overkill, but keep in mind that John was actually sick with a terminal disease and thus felt offended after discovering Mark's secret. It could also fall perfectly in line with his philosophy because from his point of view, people who faked being endangered did not appreciate the life they were granted and as such deserved to have their life put in danger, if not ended outright.
Both Lawrence and Adam cut at their chains with their hacksaws immediately once they get them. The chains are so resilient, Adam's saw breaks extremely quickly. So imagine how blunted Lawrence's is by the time he decides to hack off his foot.
