The film takes place in Gotham City.It's a geographically indeterminate urban sprawl which vaguely resembles New York and/or Chicago, dark, gothic & decaying, in which it seems to be constantly night and/or raining, not to mention its populace seems about as damned as that of Gotham.
John Doe is actually an Author AvatarThink about the various speeches he gives about his work. How it will be studied and followed forever. Fincher's basically goating to the audience through John Doe, telling us that his work (i.e. the movie) will be remembered forever. And I can't disagree with him.
Mills is gonna be killed in jail by his Wrath to complete the plan.Because of his anger he will end up in a fight with a fellow prisoner or a guard and be killed.
The victims were actually homonculiJohn Doe is actually an alchemist, who discovered these homonculi living in the world. They lost their memories, powers, and regeneration abilities because something happened to them, and he decides to kill them in creative ways
John Doe was Keyser SozeThe entire Envy persona was all an elaborate ruse for some goal the audience wasn't privvy to. His death was faked, or maybe not depending on how far ahead of the game he was.
That it wasn't Tracy's head in the box, but Mills unborn/aborted child.The reason why Somerset has to pause because it takes a while to see what he's looking at.