To be specific, the King James Bible, and I plan to go through every book in turn in my search for inspiration (though no promises whether I will ever finish it - right now, my work schedule is rather busy and this is not my only major gaming project, so updates will be rather sporadic). This is not intended to be any serious exegesis of the Bible - the goal is to mine it for gaming ideas, not trying to figure out what the authors actually meant with each and every verse, so "creative re-interpretations" in the style of +Kenneth Hite's Suppressed Transmissions will be rather common. In particular, I will focus on adding new stuff for my own Urbis setting, but that doesn't mean I will limit myself to it.
With that in mind, let's get started - with the Book of Genesis.
" And the earth was without form, and void; and darkness was upon the face of the deep. And the Spirit of God moved upon the face of the waters."
The "Face of the Deep" - an evocative image, isn't it? How about taking it literally instead of viewing it as a metaphor? What if is there are some gigantic creature or phenomenon inhabiting the ocean depths? When I came across the verse some time ago, I came up with the following for Urbis:
"A recurrent phenomenon of the Great Western Ocean are the so-called "Faces of the Deep". Observed only at night, these are large patches of illumination within the ocean depths which look like faces when seen from above from a passing ship. Often these faces are recognizably human, but just as frequently they are of decidedly non-human shape, and at times from creatures which have never been seen on Rothea. Sailors generally believe their appearances to be major omens, and have all sorts of superstitions about what kind of face will portend what fates. So far, no explorer has managed to find a Face of the Deep and to dive down to it quickly enough to discover what causes their appearance."
" And God said, Let there be light: and there was light.
 And God saw the light, that it was good: and God divided the light from the darkness."
While the very next verse makes clear that this, in fact, refers to the Day, what if we look at this "Good Light" as a separate entity? Perhaps it was the very first angel created by God? In Urbis terms, perhaps it is an elder entity mentioned in numerous mythologies and religions which can be invoked with the right rituals, with emanations of various strengths. Those who are within its radiance feel calm and peaceful, ceasing all aggression, while "creatures of darkness" (such as undead and the truly wicked) flee from it. Using Google Translate, we come up with a Greek-ish name for it - the Protofos. Many scholars believe it to be the remnants of the very first light of creation, though nobody is for certain - nobody has ever managed to communicate with it.
" And God said, Let there be a firmament in the midst of the waters, and let it divide the waters from the waters.
 And God made the firmament, and divided the waters which were under the firmament from the waters which were above the firmament: and it was so."
Waters floating above the firmament? That is, in the sky? Sure, if you want to be boring about it you could interpret that as clouds, but I think floating lakes high up in the atmosphere are more interesting. In Urbis, I already have a high-atmosphere phenomenon - the Boreal Wind, so it's not as if strange stuff floating where it's not supposed to be is unprecedented. Let's say there is a substance called "float dust" with natural buyoancy - light enough to float to the upper reaches of the atmosphere where its buyoancy is counterbalanced by the thinning air. What's more, it can bond with water, granting it the same buyoancy and causing the water to clump together until its density in the water grows too thin, which causes the water to plummet and break up into smaller clumps. Alternatively, the floating lakes can lose their water via consensation, exposing the float dust again and scattering it.
From the ground, the "floating lakes" were long mistaken for ordinary high-altitude clounds until mages actually visited them. Needless to say, floating dust is extremely valuable, but harvesting it from the floating lakes is tricky - none the least because these lakes serve as breeding grounds for high-altitude ecosystems. Many flying creatures come here to spawn, and their larvae live in the water until they grow large enough to fly on their own - which of course attracts numerous predators preying on the larvae. If a late collapses suddenly, this may lead to the infamous "rains of tadpoles" and the like.