This thread so far has been invaluable. Y'all rock.
There were two ways I could see myself pursuing a pantheon. One was a monotheistic, Sepulchravesque campaign with the idea of a Catholic-anaolgue. I didn't find this limiting at all, since it has a good deal of verisimilitude with the real world which the players could easily feel (using the word "Curia" for example). Also, examples of breaking away such as the Reformation (Calvinists) or the creation of the church of England can provide numerous ways of making politics very complex easily.
The second was a polytheistic campaign, and gets a bit more complex. Specifically, I was thinking of "The Book Of The Righteous." For those who don't know, BOTR has two new ideas -one goes on the idea of a well-accepted pantheon of good-aligned only gods reigning from heaven, as the evil ones are banished to hell (or abyss, if you prefer). The second is in the use of the great church, which is a church which worships all of the good gods equally. It does not supercede the gods own religious church but is more for the layman and promoting the idea of good in general, especially to curtail the advances of evil.
At the moment, I'm more interested in the second one since it's giving me the vibe of having the potential of being more convoluted. The history of the gods churches and the great church is left relatively open for the GM to modify as he see's fit. And looking at it from a pessimistic, cynical point of view, the potential for having it strifed with a history only humans can give is quite rich.
The gods own church can easily have different sects. The great church has different factions. Both churchs has bishops (or an equiv. title) ruling over a region or nation, thus entering in the politics of a kingdom and its king. Throw in some politics, backstabbing, and power hungry politicians or clergymen. Shake 'n bake, set in oven for a thousand years. End result could have something with the great church having an inquisition purging themselves or another gods church (wouldn't be pretty), splitting of a major faction due to politics of a nation, a people, or differing philosophical viewpoints, war between the factions, and long grudges.
But they'd all be good at heart.