"Maybe it's God inside," the Toad said in a high-pitched voice […] "Come to say he's sorry for all the sun flare business." (3.15)
Probably the only mention of God throughout the whole entire book (and quite possibly the entire series). This is pretty important, especially because the Toad is being sarcastic here.
There was a longing in many of the eyes he saw, like people truly thought they were being saved by some divine power. It made Mark feel a little sick. (3.17)
Though the Toad was being sarcastic about God saving everyone, there are people who actually believed him. Think about it: you've gone through hell and back and all of the sudden an airship is showing up at your village. Maybe, just maybe, they're there to help?
"Lucky to have a guardian angel like me to save your hide." (9.10)
Okay, we know, this isn't religion we're talking about. But having a guardian angel is a spiritual belief, despite Alec's joking tone.
Five or six people were dancing and gyrating around the bonfire, throwing their arms up and bringing them down again, bowing toward the earth and then shuffling to the side, where they started all over again. (23.17)
Is this a cute campfire kumbaya session? Nope, something weird is going on here (cough, demon worship).
"The spirits speak and we follow their orders. Since the rain of demons from the sky, we've left our village, seeking holier places." (24.23)
Deedee's village rationalizes the Flare onslaught as demons striking them down because of their sins. So basically, they turn to spirituality as an answer for the unspeakable crime.
"The world is beset with evil in many forms. And we can take no risks, especially since you invoked the name of Deedee." (24.25)
Deedee's people also think she's some kind of evil sorceress. Rightttt.
"I thought it was merely a celestial event that happened to take place in Earth's plan. Coincidence. Misfortune. Bad Luck." (25.5)
Coincidences, misfortune, and bad luck—these, believe it or not, are all examples of spiritual ideas. No, they aren't religious by any means. But they are forms of superstition.
"Both times it came from the heavens—once from the sun, once from the ships. We think they may visit annually, to punish us for becoming lax and to remind us of what we need to become." (25.7)
Okay, so clearly these people are crazy. The point is, when people are put through awful times and they can't possibly provide an answer as to why, they often turn to some form of spirituality.
He moved out of the direct view and leaned on the wall, looking around as if some magical weapon might appear in front of him. (41.6)
Looking for something that isn't there? You're invoking some kind of chance or coincidence to happen, therefore being slightly spiritual.
All eyes were on Trina, as if she had some magical, hypnotic power. (58.5)
Yeah, this is the weirdest scene in the book. People infected with the Flare often have crazy thoughts of spirits and magic and such. In this case, when Trina yells for everyone to stop, they look at her as if she's some kind of goddess.