multiple gangs (Gotham is the third for mundane crime. Hub City and Bludhaven are numbers 1 and 2),
barely legal tax haven laws,
a literal hell gate,
16 sealed greater demons (a demon lord and their court. They are in most canons buried under Arkham and spread a corruption that encourages the seven deadly sins),
first for both police brutality and corruption,
Scarecrow fear toxins in the water (at low enough levels, it only causes paranoia),
an old God's corpse (this old god is leaking forbiden knowledge that causes people to lose their humanity slowly and do ever more depraved acts in pursuit of knowledge),
a living old god who is bat themed and has his own underground Gotham city,
Dracula either moved to Gotham or had his tomb forcibly moved to Gotham,
built on the grave/resting of a warlock (Adam Gotham), who is both alive and dead at the same time (cursing the land to be a place of constant misery),
a very tough and kind of cruel college that creates super villains (a lot of the Batman rogues gallery got their diplomas there),
massive government corruption,
a smog problem so bad that the Flash can't run at full speed without wheezing,
Joker chemicals in the water,
Lazarus pit run off in the water,
Marsh of Madness runoff in the water (this marsh causes delusional homicidal madness),
Slaughter Swamp runoff in the water (this swamp causes violent undead and preserves life in a twisted mockery of all that is holy),
evil floating in from the Jersy Pine Barrens (this evil floating in decreases empathy and encourages devilish behavior. Also, the Jersey Devil may occasionally hunt in Gotham, but his might just be urban legend in Gotham)
pollution due to being in a barely regulated industrial zone (it is legal to dump industrial runoff in Gotham River),
multiple mad scientist labs legally there (Gotham intentionally has very few laws mandating ethics or limits of research),
the location of a crack in the door to the afterlife,
the line between death and life is really fuzzy (this makes it harder to die),
is the second most haunted city in DC USA (they kept New Orleans as most haunted)
a strange aura weakens green lantern power constructs,
built on a Indian burial ground,
A dysfunctional legal system (with no death penalty, so everyone goes to either Blackgate or Arkham),
cursed by an ancient shaman,
run off from an unnamed well that causes increased physical abilities in exchange for homicidal violent impulses (aborted Bane plot thread from before they decided Bane should just use chemicals in his Venom),
trace amounts of Bane Venom in the water,
666 minor demons who just live regular lives with regular jobs while waiting for the apocalypse (Baytor is the most famous and is a bar tender to make ends meet),
cursed by Zeus (this curse is why Gotham has, on average, 320 days of rain or overcast skies each year),
unusually vicious mutant rats,
mutant sewer alligators,
mysterious ruins from a lost civilization that the sewers run into (the sewer alligators breed there),
blessed/cursed by a nature godess to keep the toxic stuff in,
a summer home for the King in Yellow (this is a rumor from the Bat Old God. To my best knowledge, the King in Yellow has never directly appeared),
a door the various old gods came through that is mostly shut (emphasis on mostly),
a massive active fault line,
a magic well,
it is slightly radioactive due to a poorly maintained nuclear power plant (it is still within habitable limits),
a weak dimensional wall allowing influences from the Phantom Zone,
a chaos well,
a bottomless pit under part of Gotham that leads to the abyss (also, the being in the abyss occasionally like to watch Gotham),
Gotham River and Bay water is so polluted that Aquaman can't swim in it,
the tap water barely is considered water by Aquaman's hydrokinesis (and Aquaman can manipulate soda, which is 90% to 95% water. Gotham tapwater is more or less sludge),
Gotham tap water is barely purified river water (mainly because if the water treatment plant gets too Gung Ho and purifies the water too much, they get a black liquid that is extremely dangerous. So Gotham City Counsel decided to only have them clean the water until it was probably reasonably safe-ish)
an evil real estate agent who sells failed amusement parks, theaters, and other buildings to criminals,
so many lead pipes or paint that Superman can't see through most Gotham homes (also note that at one point, the fumes from leaded gasoline blocked Superman, but hopefully that problem has gone away),
an Atlantis Leviathan who is fated to flood the world under the docks (there is apparently seven of them and the Atlantic ocean's is under Gotham),
most of the city is slightly radioactive due to a failed nuclear power plant (Gotham is still within habitable limits. Note that this is a different power plant from the still active but poorly maintained nuclearpower plant),
Gotham, as in the city itself, is aware and has an unhealthy interest in the Bat Family (Tim Drake in particular),
5 different cults,
at least 2 different shadow governments (the line between cult and shadow government is weak in Gotham. I put the Court of Owls and League of Assassins in this group),
and worse of all, it is in New Jersey (try reading a Batman comic and give everyone a Jersey accent).
