5. Moe not only enables, but DIRECTLY CAUSES Barney's crippling alcoholism
As the Movementarian cult falls apart at the end of The Joy of Sect, Moe reluctantly decides to return to his one true faith: voodoo. Although that means we'll mostly have to ignore Moe's previous claims about his faith: Possible causes of alcoholism.
And in this act, Moe reveals that his relationship with Barney is MUCH MUCH darker than we originally thought: not only is Moe constantly overserving and enabling the worst alcoholic ever portrayed on television, but he may be using spiritual powers to keep him addicted to booze.
Barney's alcoholism has always been a weirdly dark undercurrent to the show - he has a legitimate addiction that has destroyed his life, but it's played for laughs (and it IS usually extremely funny, but that doesn't mean it's not also kind of horrible). Prior to this, it was clear Homer and Moe were both enablers for Barney (never really pushing him to confront his VERY REAL alcoholism or suggesting it may be causing damage to him), but now it's clear that Moe actively seeks to find ways to ensure Barney REMAINS an alcoholic.
Pretty impressive for an episode satirizing cults and Scientology to mine its darkest joke from something else.
6. The impossibly sad reality of Homer and Marge's marriage
The marriage of Marge Bouvier and Homer Simpsons is not a balanced one - Marge devotes herself entirely to supporting Homer and the rest of their family, and Homer responds in neglecting the family (and Marge) as frequently as possible. He's irresponsible with money, constantly selfish with his time (often spending nights at Moe's while Marge watches over their three children), frequently lies, and generally takes Marge for granted every waking moment of the day.
Causes of alcoholism and drug addiction
And in Secrets of a Successful Marriage, Homer begins to recognize this sad fact - but greets it with joy instead of horror and regret. When trying to think of one good reason why Marge should want to be with a rude, thoughtless, alcholic lout like Homer, the best he can muster is that he needs her more than she needs him:
"Complete and utter dependence." The darkest thing here is that Homer's right - that IS all he can offer her. He doesn't appreciate what she does for the family, he doesn't care that she gave up her entire life for the family she's built wiht him, and he treats her and her concerns with complete indifference. She offered him everything, and he gives almost nothing back in return. Really, no one deserves to be married to Homer Simpson - and both he and Marge know it.
7. The psych-out death of another family
While the last one was a bit more of an existentially-grim joke regarding the total journey of Homer and Marge as characters trapped in a grotesquely one-sided marriage, here's a more straight-forward bit of darkness - in Itchy & Scratchy Land, Homer's driving the family to the titular theme park, although a long night of driving has left him obviously exhausted:
The scene immediately cuts to a car skidding after poorly taking a turn, smashing into an electrical pole, and bursting into the a bit of a twist:
The joke, you see, is that it WASN'T the Simpson family who perished in a fiery wreck, but someone else! And while it's KIND of funny that the editing tricked us into briefly believing the Simpsons died in the middle of an episode, it's also INSANELY DARK that the show basically just killed some other random family for the sake of a quick little gag about Homer driving while sleepy and accidentally killing the Simpsons.
8. 22 Short Stories About Springfield reveals Herman's a much darker character than we realized
There's a few bits in 22 Short Stories About Springfield parodying the (then recent) Quentin Tarantino film Pulp Fiction - and at first, they're pretty harmless: a quick Misirlou sound cue to making fun of the "Royale with Cheese" conversation and revealing Krusty Burger has obscenely literal names for all of their products:
So at first it seems like they'll probably be focusing in on the Vincent Vega / Jules Winnfield segment - until Wiggum has a run-in with Snake, and their street brawl spills into Herman's Military Antiques - where it becomes clear that we're now cleanly in the Butch / Marsellus Wallace segment. And if you're familiar with THAT sequence in Pulp Fiction, this image should make you EXTREMELY UNCOMFORTABLE:
For those of you who have somehow gone your entire lives without ever watching Pulp Fiction, this is a direct reference to a scene in Pulp Fiction where two enemies - an aging boxer and a mob boss - accidentally get captured by a weapons seller weirdo when they stumble into his store, and he proceeds to invite his friend (named Zed) over so that the two can take turns raping their kidnapped victims. That's right - the implication here is that Herman (and Zed) are going to sexually violate both Chief Wiggum and Snake.
Causes of alcoholic liver cirrhosis
In the film, only Marsellus Wallace is actually assaulted - Butch manages to wrest free of his constraints, grab a samurai sword, and attack their captors and free Marsellus. Luckily here, Milhouse and an ill-timed bathroom visit manage to take out Herman before anything THAT dark can happen. But still, it's clear what Herman was planning, and suddenly his character has moved from "war-obsessed oddball" to "sociopath rapist."