I think I'd approach it from a different direction: figure out cinematic/storylike things that commoners might pray for, and then work the powers backwards from there.
Here are some examples:
* "Cuthbert, protect me from this marauding vampire!" The commoner develops a one-shot negative energy protection: when the vamp attacks, there's a burst of positive energy, enough to drive the vampire hissing into the night.
* "Pelor, have mercy on my sick child!" The child makes his next two saves vs. disease, curing him and setting him back on the slow road toward health. However, the child is then marked for the priesthood: his life is Pelor's now.
* "Hextor, my neighbor has been sleeping with my husband: destroy her!" A raiding party of orcs comes to the village that night, killing both the neighbor and the worshipper.
I'd make these prayers a once-in-several-lifetimes experience: most people will never have a prayer be answered. When they are answered, they may be answered dramatically (as with the vampire), subtly (as with the sick child), or monkeyspawedly (as with Hextor). They should be governed by plot-devices, not by rules: basically, the NPCs are giving up their wills to the Gods, and the gods are responding.
Anyone who can call regularly on the aid of the Gods ought to be called a cleric, I think. I might consider the most faithful commoners actually to be 0th-level clerics, able to access a few orisons, maybe limiting the orisons by the god's domain.
As for graveyards, in a world with standard D&D magic, most folks won't have access to individually-blessed gravestones. They're magical items, too expensive for most folks. A graveyard might receive a seasonal blessing, however; a typical blessing would prevent the bodies contained within from being raised as undead. There might even be an annual festival in which a cleric casts a ritual that results in a mass speak-with-dead, allowing mourners to exchange a few words every year with their departed loved ones.
For wealthier folks, a bestow-curse tombstone would be a great thing. Alarm stones might be placed in tombs, if there's going to be a cemetary guard. And a gravestone that contains a once/week (or once/month on the new moon, or once/year on All Hallow's Eve) speak with dead would be pretty cool; a king might order such a tombstone for the wisest of his advisors, and the effect might remain centuries after the kingdom has fallen.
Daniel