I use the Greyhawk gods, but I put them into custom pantheons that fit my Renaissance Europe setting. Without going into too much detail (unless you want more detail, in which case I'm happy to indulge you!)...there are two main religious factions for the players: the Old Faith, and the Temple of Dawn. A third, The Fell Gods, is a collection of evil cults and fanatics, and isn't typically open to players.*
The Old Faith is the preferred religion of druids, firbolgs, elves, and outlanders. Light on the dogma, heavy on oral tradition, thousands of years old, it's a thinly-veiled analog for Paganism. The pantheon is led by Obad-Hai, and includes Ehlonna, Fharlanghn, and Boccob. They don't have grand temples; they have sacred enclaves and groves, and small roadside shrines.
The Temple of Dawn is the highly-structured, dogmatic religion of paladins, clerics, humans, and cloistered monks. Heavy on dogma and the written word, and comparatively new in the realm, it is a thinly-veiled analog for Catholicism. The pantheon is led by Bahamut, and includes St. Cuthbert, Heironeous, Pelor, Yondalla, Kord, Moradin, and Corellon Larethian. They have large, magnificent temples that serve the community as libraries, schools, and--in times of crisis--hospitals, orphanages, and garrisons.
The Fell Gods aren't organized or united under a single pantheon...they are all individual cults, each one trying to outcompete the other. The Cult of Nerull, the Cult of Tiamat, the Cult of Lolth, etc., all fall under this one umbrella term.
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*if a player wants to worship one of these gods, they have to make special arrangements with me first, so that I can shape an interesting story around them. I have special backgrounds ("Former Cultist," "Redeemed Heretic," etc.) for them and everything. So far, no takers.