I recently decided to include Clerics in my game (currently that's not the case) and, as part of figuring out how I want to do this, posted a question about creating pantheons on Google+ and got some good responses and also a few links to Alex Shroeder's blog where he outlines how he's been running deities and Clerics in his games. I found his post about reputation especially interesting. I've reworked it a little bit and present it below. Along with tracking the alignment of my players, I'm hoping to expand this system and to use it not only for Cleric PCs' religious standing but for all PCs' standings with different factions or NPCs.
Clerics begin play with a reputation rating of 1 with their deity. At the end of each session in which a Cleric has performed an act on the following table, the Cleric’s player rolls the die that corresponds to the most significant act of the Cleric that day; if the rolled result is higher than the Cleric’s current reputation score, the Cleric’s reputation score increases by one.
d4: Fulfilled intermediate tenet of faith or service related to single believer
d6: Fulfilled major tenet of faith, service related to single local congregation or saved life or body of single believer
d8: Related to single order or sect, saved lives or bodies of single local congregation
d10: Related to whole religion or a servant of the god, saved lives or bodies of entire order or sect
d12: Related to the god, saved the lives or bodies of whole religion
Losing reputation is easier and more drastic than gaining reputation. At the end of a session in which a Cleric has blatantly violated a tenet of the Cleric’s faith or done an active disservice related to the Cleric's faith, the Cleric’s player rolls the die that corresponds to the act of the highest magnitude of the Cleric’s that day. The number rolled on the die is subtracted from the Cleric’s reputation score; in this way, negative reputations are possible.
If the Cleric has performed both reputable and disreputable acts within a single session, increase the disreputable die size by two and compare the two dice; subtract the smaller die’s sides from the larger die’s sides and roll a die with the number of sides that results, applying the result towards or against the reputation in correspondence to whether the larger die was reputable or disreputable.
For example, Kolath the Cleric of Zeus, within a single session, stole some gold from a member of the congregation of the local temple of Zeus and also helped the rest of the party fend off an army of goblins intent on killing the entire local town. The theft from the fellow follower of Zeus corresponds to the d4 and saving the town, which includes the local congregation of Zeus, corresponds to the d8. Adding two to the four sides of the d4 and subtracting the resulting six from eight leaves a d2 for Kolath's player to roll to see whether Kolath's reputation rises with Zeus or not. Unless Kolath's reputation with Zeus is already lower than 2, Zeus is so non-plussed with Kolath's theft that even saving an entire congregation is not enough to impress Zeus.
Reputation with one's deity is important because Third through Seventh Level Cleric Spells are granted to Clerics by higher powers. In order for spells of a certain level to be granted to a Cleric, the Cleric must both be of sufficient level to have spell slots of that level (like the "normal," as-written Cleric in most systems) and must have a reputation rating with the higher power of at least the same level as the spell.