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").
Asspull: Somerset just happens to know a guy from the FBI that is in his debt for no discernible reason. Thanks to the info they get from him, they are able to instantly find John Doe's apartment and even John Doe himself when he comes home.
Possibly justified since he is nearing retirement and probably has a lot of potential contacts and markers he can call on.
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 be 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. The only point of debate for whether he qualifies for this trope is that he might be considered so utterly insane that morality truly cannot be applied to him.
"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.
Ho Yay: Lampshaded a couple of times. When they're waiting for Somerset's FBI contact, Mills asks why they couldn't sit opposite each other because sitting next to each other makes it look like they're dating, and near the end there's a scene where they're both shaving their chests, and Mills jokingly comments that if he keeps coming home late, his wife is going to get suspicious.
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.
The horrifying Jump Scare of the "Sloth" victim has likewise lost a lot of its power due to this.
Moral Event Horizon: While most would consider John Doe to have crossed this with his very first murder, in his view his victims were not innocent so those killings were justified. However, Tracy was completely innocent of everything, so even his own twisted standards couldn't have excused his last killing.
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, Eight MM, was a rather obvious attempt to recapture the mood and tone of it).
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."