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.
And angels, and the nature of man, and the Prophets, and other celestial beings... Hell, even The Bible is interpreted in a decidedly un-Catholic way. (Specifically, no, indulgences do not work the way the movie says they do, but the Protestant interpretation of Matthew 6:19-21 explains how Dogma's indulgences work. This is lampshaded in the airport scene.)
Of Hell, instead of being a place of damnation for horrible people, it is for people with huge Heroic Self-Deprecation that God can never forgive them so they opted to take eternal suffering for their guilt.
Anticlimax Boss: The Golgothian, Hell's top assassin is taken out with a can of deodorant.
Anvilicious: Many of the ideas proposed in the film about organized religion and the nature of spirituality are worth serious consideration. They still come down very heavy-handed.
Awesome Music: "Still" by God Herself, played over the end credits.
Nun: Let me get this straight: you don't believe in God because of "Alice in Wonderland"? Loki: No, "Through the Looking-Glass". That poem, "The Walrus and the Carpenter," that's an indictment of organized religion. The walrus, with his girth and his good nature, he obviously represents either Buddha, or, or with his tusks, the Hindu elephant god, Lord Ganesha. That takes care of your Eastern religions. Now the carpenter, which is an obvious reference to Jesus Christ, who was raised a carpenter's son, he represents the Western religions. Now in the poem, what do they do? What do they do? They, they dupe all these oysters into following them and then proceed to shuck and devour the helpless creatures en masse. I don't know what that says to you, but to me it says that following these faiths based on mythological figures ensures the destruction of one's inner being. Organized religion destroys who we are by inhibiting our actions, by inhibiting our decisions out of, out of fear of some, some intangible parent figure who, who shakes a finger at us from thousands of years ago and says, and says, "Do it... do it and I'll fuckin' spank you."
Moral Event Horizon: Bartleby orbits it for at least a third of the movie, but unequivocally crosses it when he taunts Bethany and sticks a shiv in Loki, not only killing his friend but doing the deed without Loki entering the church, knowingly condemning him to Hell.
Narm: Perhaps the most dramatic scene in the film where Bethany discovers she's descended from Jesus' family is wrecked a bit by her soaking wet sweater clinging to her breasts.
Squick: The Golgothan, the demon made of... human excrement. If you ever plan to eat again, just skip it.
A second appearance of the demon was deleted.
Tear Jerker: As mentioned below, Bartleby meeting God once again since thousands of years ago and breaking down in tears. It only makes the punishment he deserves tragic... a little bit at least.
Silent Bob crying as he carries Bethany's dead body. Even Jay shed a tear over this. Thankfully, she's brought back to life.
Bethany realizes the Awful Truth: She must kill the angels Bartleby and Loki. She runs into the woods and falls into a creek, flailing at the water as she cuts loose a Rage Against the Heavens. The Metatron arrives in response to calm her down, which leads to Bethany collapsing weakly into the water, weakly protesting against her quest.
Bethany: I don't want this, it's too big.
Metatron telling the story of how he had to inform Jesus about his destiny.
"I had to tell this 12-year-old boy, who wanted nothing more than to play with other boys, that he was God's only son, and it would mean a lifetime of persecution and eventual crucifixion at the hands of the very people he'd come to enlighten and redeem. He begged me to take it all back, as if I could. But there's something I've never told anyone. If I did have the power, I would have."
Unintentionally Unsympathetic: Despite her very unfortunate marital history combined with the craziness going on around her, Bethany is far from a likable character.
He was the one most sympathetic to and fond of Humanity, a viewpoint he held from Biblical times up until that night on the Jersey-bound train.
Bartleby breaks down in tears when he sees God again for the first time in several millenia. That's when you realize that he is essentially a child who has been abandoned by his mother.
He feels this way about Jesus, after he told him how his life would turn out: "He begged me to 'make it all not true'... If I had the power, I would have."
Metatron is something of a Stoic Woobie: He's had to deliver some truly awful messages to humanity over the course of history, and now people are drenching him with the contents of hand-held fire hydrants. He never complains, but still, it's hard not to feel sorry for him.
Loki. His job aside he was one of the nicer angels even hung out with Jay and Bob before knowing they are prophets. When he finds out Bartleby is more focused on war on god than going home, he becomes more sympathetic, even cutting off his own wings and trying to stop his former friend. It doesn't end well.