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.
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. Followed by the Metatron telling the story of how he had to inform Jesus about his destiny.
Bethany: I don't want this, it's too big. Metatron: That's what Jesus said. Yes, I had to tell him. And you can imagine how that hurt the Father - not to be able to tell the Son Himself because one word from His lips would destroy the boy's frail human form? So I was forced to deliver the news to a scared child who wanted nothing more than to play with other children. I had to tell this little boy that He was God's only Son, and that it meant a life of persecution and eventual crucifixion at the hands of the very people He came to enlighten and redeem. He begged me to take it back, as if I could. He begged me to make it all not true. And I'll let you in on something, Bethany, this is something I've never told anyone before... If I had the power, I would have.
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.