I actually made an account to post a topic just like this an lo! it was there. Well, here's how I could see religion going in. First of all, the item that a temple is centered around would be the altar. Built like a bed, table, chair, whatever, the altar is where you set the size of your temple. Now, there would be several altar types that would be selected much as we now select different workshops. Let's say, oh, eight gods (as Pratchett fans will recall, 8 is a powerful number). You have your basic elemental gods and their opposites: light/dark(or life/death) fire/water air/earth order/chaos(also known as blood...). Now, each altar would have certain requirements/effects. The dark altar may require sacrifices, the chaos alter may require GENEROUS tithing, the water alter may require a channel or the river be run through it, air may have to be built outside, fire near magma, I think you get the idea.
Now, you have your altar and you've met its requirements, now what? Well, now your dwarves will congregate upon the temple of their choosing. Will you dedicate your fortress to one deity or allow all religions to prosper? Your choice, of course. Nobles may demand that an altar be built, migrants arriving with religious preferences (found the same place you find out what their favorite stone is) may become agitated at the lack of proper spiritual facilities, traders may jack up their prices because of your heathen practices, who knows?
Speaking of nobles, the third and most important part of this would be the High Priest noble. If your temple is doing particularly well (sacrifices made on time, lots o' coins put into the box, multiple or high ranking nobles visiting a temple often) you will be graced with the presence of the High Priest of that temple. Well, what does he/she do? Simple, what every other noble does... make stupid demands. Allow me to illustrate:
My fortress "Doom Cushions" is doing well. I'm fairly early on in it's life and have only 30 dwarves living there. One of the first buildings I built was a temple to the water goddess "Bluelighting" (random deity names, of course). The altar required that it be built on a channel of water, so I have a room like this:
code:
#|###|#
#| |#
#|_X_|#
# #
### ###
_ & \ = channel
# = wall
X = altar
Well, now the High Priest for Bluelighting shows up and demands there be two statues in there. Maybe demand a certain material. So now I need this:
code:
#|###|#
#| |#
#|_X_|#
#S S#
### ###
_ & \ = channel
# = wall
X = altar
S = statue
Eventually this temple just wont do, because as the number of followers increases (along with the donations, happiness provided to followers, and of course the number of staff and their wages), the temple will have to become much larger/more detailed. Darkness may require more sacrifices or even DWARF sacrifices (Tobul cancels sleep: being dragged to altar).
And finally (I know, right?) I think it would be best if there were no REAL effects to the religions. Have it all be on the followers. If worshippers of the fire deity are able to summon up their god to exact revenge it leads to a sort of magical "my god can blow stuff up better than your god" kind of thing. Dwarf fortress, to me, isn't like that. It is more of a "my god is better than yours and I'll convince of this by using sharp objects" sort of thing.
However since magic is planned, it COULD be based around this system where as you gain the deity's favor you are more able to control its magics.
But that seems like it should be another post.