These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Well, from his diaries, we know that Doe is the type of man who would vomit on a guy who just asks him about the weather and laugh about it because he finds the average human being absolutely disgusting, so its not quite the same thing. Both believe they live in a Crapsack World, but Doe believes that because he is a completely egotistical bastard who ignores his own rampant hypocrisy, so he's not really an Only Sane Man (not by a mile) so much as Right for the Wrong Reasons (for a really, really cynical interpretation of "right").
Complete Monster: John Doe is possibly the most twisted and disturbing Serial Killer in film. The reasons for his actions defy understanding. Judging from his diary entries and speech in the squad car, it can argued that Doe's actions are rooted in a deep disappointment with humanity that warped into extreme misanthropy, which doesn't change the fact his torture/rape/murders are completely horrifying (especially the last one, which is inexcusable from any standpoint). Because it would be unimaginable to actually show these crimes onscreen, only the gruesome aftermath is seen.
More generally, though: it's been raining in the city for nearly a week and it's implied the city gets a lot of rain. At the climax of the movie, our heroes head out of the city into the immediate environs... which are a flat desert that behaves as though it hasn't seen rain in months*
The victim of the Lust killing is not actually guilty of the crime of lust herself. Lapse into lazy writing and casual misogyny on the part of the screenwriter, or apt characterisation of John Doe as a woman-hater himself who of course would blame lust on the prostitute rather then the men she services? Your call, viewer.
You could argue that the john is the true intended victim, as now he'll have to live with that memory.
It's also possible that John Doe blamed Lust for enabling other people's sins.
Given that Doe later calls her a disease-spreading whore, rampant misogyny on his part seems the right call here.
"Funny Aneurysm" Moment: Mills and Somerset panicking over the legal implications of the FBI secretly tracking potential criminals via certain books taken from the library, and their use of said evidence to track down John Doe. In an age where the War on Terror and the rise of the Internet has turned that kind of thing Up to Eleven, it all seems rather quaint.
It Was His Sled: People who don't know who plays the villain, or what happens in the dénouement, are pretty hard to come by.
Narm: Brad Pitt bleating out "What's in the boooox?" like a kid whining that he wants a cookie.
Nightmare Fuel: All five murders to differing extents, especially Sloth.
Narrowed It Down to the Guy I Recognize: Ingeniously averted. The name of the guy you recognize doesn't appear on the poster or in the opening credits, and you don't get a clear shot of his face until the third act.
Tough Act to Follow: For screenwriter Andrew Kevin Walker. No screenplay he has penned since this one has achieved anything like the kind of critical acclaim and commercial success heaped on Seven (the screenplay that immediately followed it, 8mm, was a rather obvious attempt to recapture the mood and tone of it).
Unfortunate Implications: The only explicitly Jewish character in the film, the lawyer Eli Gould, is murdered because he is so greedy. That being said, it's not inconceivable that John Doe is anti-Semitic on top of everything else.
It also ties in with his obsession with Christianity, too. A lot of Christians believe that the Jews killed Jesus, or that since they don't believe he even existed (he just hasn't visited yet, according to their beliefs) they "hate" him. Kinda like how some Christians say that they only think that Atheists don't believe in God/Jesus because they hate them.
What The Hell, Casting Agency?: Or in this case, WTH Promotions. David Fincher mentions in a commentary track that for reasons he cannot fathom, the people who went out looking for test audiences for the movie used Driving Miss Daisy and Legends Of The Fall as examples of movies that Morgan Freeman and Brad Pitt, respectively, have been in. So naturally, most of the people in the audience were the kind of people who would watch films like Driving Miss Daisy and Legends Of The Fall, and not films like, well, Se7en. Fincher said that after the movie got out, he was standing outside the theater, and three middle-aged women walked past him. As they did so, one said "Whoever made this movie should be shot."