In my current campaign, the Gods are organized into a loose pantheon, divided into three sub-groupings, the Gods of Law, Neutrality, and Chaos. However, this was not always the case- not all deities have similar origins, and there are minor gods who are not recognized as members of the pantheon (though some might actually be other gods in disguise). Ending about 500 years before the current time, there was a centuries-long war among the gods, when the Gods of Law did battle with those of Chaos, and the Neutrals were soon forced to choose one side or the other. A lot of Gods "died" in the process- either actually dying, or simply having their connection to the world severed (in the case of deities who are worshiped on other worlds, such as Lolth).
Syncretism runs rampant in the setting as well- if different Gods are worshiped in, say, the Iron Kingdoms to the south than in the Bordermarch of the Freeland, they could simply be the same Gods under different (or assumed) names, though most cosmopolitan characters (such as the PC's) can pretty quickly look at the faith of two differently named gods and realize "say, those two are the same guy", even if the populace might disagree.
I also use the 4e term "exarch", where a deity might have subordinate deities as well- to the point that worshiping the exarch is the same as worshiping the main deity. One of the "Gods" of Neutrality are The Brothers, twin deities who are basically exarchs of one another- you can't really worship one without the other, as, despite being two individuals, they are effectively one God.