Jay's massive rant at the climax is side-splitting from start to end, but peaks with his angry shout of "WHAT THE FUCK HAPPENED TO THAT GUY'S HEAD!?!" Witness it here.
And then the power of God's kiss overwhelms Jay so much that he passes out.
Loki's Establishing Character Moment in the opening when he tells a nun how Alice in Wonderland is responsible for his lack of faith in religion due to him seeing the story of the Walrus and the Carpenter as a commentary on the subject, the two representing the deities of the earth who fool the oysters into following them before they shuck and eat them. Funny because as ridiculous as it is, his explanation sorta makes sense — indeed, the idea of the poem as an attack by Lewis Carrol on religion is a common theory bandied about when the symbolism of the piece is discussed.
Especially the conversation that Bartleby and Loki have afterwards (paraphrased):
Bartleby: "You have been in God's presence. He has spoken to you personally. Yet I just heard you claim to be an atheist."
The diner conversation when Jay and Silent Bob think Bethany is going to sleep with them.
Jay: "So do you do anal? Is it true that chicks fart when you blast them in the ass?"
The Wheaties-like cereal Hosties in the background of the scene in Glick's office. It even has a picture of Jesus posing how athletes do on Wheaties boxes!
Also from the office scene:
Rufus: We were sent by Him who is called I Am!
Glick: Cute. Playtime with the cardinal's over.
Rufus: (stumped) Worked for Moses.
After Jay accidentally makes Bethany realize that John Doe Jersey is really God, trapped in human form:
JAY: (with his pants down) What am I supposed to do [to stall Bartleby]
BETHANY: Think of something!
JAY: I already did, but it takes two of us!
George Carlin as a priest!!!
Metatron beginning to wipe Bartleby's remains from his coat with a fold of God's dress and then stops, realising what he is doing, all the while God just stares at him blankly.
The scene where Azrael tells off the Stygian Triplets for failing to kill Bethany. The fact he doesn't even sound angry, just annoyed and disappointed, and the way the triplets react, makes it more like a dad telling off his kids for breaking a window while playing soccer. And, at the end of that scene, the way the triplets react when Azrael talks about summoning the Golgothan.