I like the way it is handled in Eberron. There is one main pantheon (though the book splits it into two, the Sovereign Host and the Dark Six, which is sort of a good/bad split), and most people worship all the gods as the situation calls for. You can even be a cleric of (half of) the whole pantheon at once. In addition to this main pantheon, there are a number of specialized religions (the Silver Flame, the Dragon Below, the Blood of Vol, the Path of Light, and the Undying Court). These don't worship gods per se, but more ideals or groups of not-quite-divine beings. They're also distinctly minority religions, and many have a major presence only in certain areas or among certain segments of the population (the Silver Flame dominates in Thrane and is viewed sceptically in other places, the Path of Light is pretty much Kalashtar only, and the Undying Court is only worshipped by the Aerenal elves).