I just browsed the Players Guide for the 3rd ed setting Kingdoms of Kalamar. In the chapter on clerics it had some options I found interesting. Those who have followed me through the years know I have a soft spot for KoK, and this was something I felt could be imported to other games.
You know how clerics can turn undead? In newer editions of D&D, that it because the channel some kind of positive energy from their god. That sounds kind of iffy to me, but you can take the concept and run with it.
If your cleric is channeling power from the gods when casting spells (from a spell list that is mostly identical to all), why not take one effect that conceptualize the area of influence of that god, and make that a power of the cleric?
So, a cleric of the god of merchants should be able to channel the power of smooth talking, charming or something similar. A cleric of the god of death should be able to somehow be more deadly once in a while. A cleric of the god of love could... Well, you get the idea.
How about that?
You could make it happen on a d20 lower than the character level, on a 1 in 6 or just once every session. Scalable to every power setting. Also, if the death channeler just gets +1 dmg or kills outright is also one of those "setting dials". Even a +1 could be fun. Everyone likes to be somewhat special.
You say it sounds like those fiddly "daily" powers from my post on old school "feats"? Yeah, it will take some bookkeeping unless you make it happen just once every session. Everyone should be able to remember if they have used their power this night, unless very drunk while gaming, right?
Then you could just tweak the spell list to be unique for every god/temple/whatever. I think the power channeling idea is more fun, though.