I have two ideas I'm toying with in regard to a more animistic cosmology in D&D, with some inspiration from the Norse/Celtic/Slavic (and some African) mythology.
The first is about Elves. Rather than being a demihuman race, "normal" elves are spirits/fey, and not a playable PC race. However, the playable "elves" are actually Changelings, that is Elven/faerie babies placed in cribs of Humans when the Human baby is stolen by the Fey. So they are, actually, fey/spirits raised by Humans, with foot in each world. This is why magic comes so naturally to them. Alternatively, they may be the offsprings of Humans who mated with minor "gods"/spirits/fey. They should have an uncanny, inhuman side in addition to their Human upbringing.
The second idea is about magic items, especially powerful and/or permanent items. Forging such items would require, for the very least, for a spirit/"god" to invest some of its essence in the item; really powerful items would have to be inhabited by a spirit/"god", either willingly or unwillingly. A relic sword might actually be imbued with the very soul of a legendary hero, and the skin of a dragon is no less than the skin of a god! Learning about the item's spirit and finding ways to interact with it may unlock the hidden secrets and new powers of the magic item.
EDIT: I have an interesting idea for my Wounded Gaia setting. During the steampunk-ish Age of Blossom, the great Magineers created mighty contraptions based on advanced spirit-binding techniques. Essentially, they forcibly trapped elemental spirits/"gods" in special clockwork receptacles, forcing the spirits to serve for eternity (until the binding is dispelled) as energy-sources for machines. The most common contraption was the Boiler of Endless Steam, where a fire spirit and a water spirit (a Salamander and an Undine?) were bound to the same spot, endlessly producing a stream of hot steam and causing unimaginable suffering to both spirits; this allowed for very efficient steam engines without the need for fuel or added water.
Of course, the spirits who broke free from such entrapment are typically VERY pissed off at mortals and might become extremely vengeful!
