Historically, the issue of religions in fantasy gaming has always been somewhat controversial; the idea of characters worshipping strange gods has attracted all manner of attention over the years, though less so of late. (And sales decline as a result; perhaps we should start trying to attract such controversy again.) More to the point, I have always found religion to be the hardest part of setting creation, hardest to be original. What I have traditionally done in my games is divided into three categories by alignment; 'Law' is essentially early Christianity with some of the names filed off, 'Neutral' is nature worship and Druidism, and 'Chaos' is a collection of semi-random cults.
That was my starting point here, but I was determined to do a lot better than I had in the past. I briefly considered using a real-world pantheon, but opted to take new ground, and then decided that I would try and do something a little different. Law, Neutral and Chaos would still be the starting point I would use, but instead of using actual 'gods', I decided instead to go with the concept of worshipping 'primal forces', my spin on 'element worship', perhaps. Instead of having a pantheon of deities covering a different aspect of the world, there would be two 'elements' that would be engaged in constant battle for control. Magic and Nature.
Magic is the Lawful side; it seeks understanding, order, and logic in the universe. This heads down the 'magic as science' angle to some extent, but I think that works fairly well in any case; after all, there are rules for magic in the books, and it seems sensible enough that there are forces that regulate them, deep in the primal nature of creation. This also explains why clerics have spells, of course; clerics and mages are two sides of the same coin, with arcane and divine magic in this setting stemming from the same source. Wizards are more focused on experimentation and research, going deep into the primal forces and studying them for greater powers; Clerics on utility, on harnessing these powers for good.
The Neutral side remains Nature, exemplified by the Druids. They seek to maintain the balance of life, and worship the cycles of eternity, the ever-changing seasons, serving as the guadians of knowledge and wisdom of the nature of life itself. Humanity is a part of life, of course, and therefore they are not anti-civilisation as such; they simply recognise that there is far more to the world than just that, and that nature also must be protected and revered.
As for Chaos? Well, there are Daemons in the rules for a reason, and each has its cults and worshippers who seek to bring it into the world. They are dependent on their worshippers, and are therefore created of the fears, dreams of lusts of those who dare to conjure them, and the more powerful their worshippers, the more powerful the daemon. Some of them have influence on reality, breaking out of the hellish dreamscape they rule, and some are even strong enough to walk the world – and when that happens, devestation and death follows in their wake.
As for the other races? Well, Elves would follow the druidic code, almost certainly, but their interpretations would be different enough to amount to a religious schism; and their magical abilities would mean that some 'heretics' would follow the worship of magic. Dwarves, I think, are Elementalists – they believe in the power of the four elements, Earth, Air, Fire and Water, and revere them in their own way. Halflings have ancestor worship, celebrating great heroes, and Gnomes are divided between the Elements and Magic. I'll break this all down more accurately before play begins, but this is where my starting point is for the present.