it depends on the wording of the spell but usually no, for instance in prayer:
"You bring special favor upon yourself and your allies while bringing disfavor to your enemies. You and each of your allies gain a +1 luck bonus on attack rolls, weapon damage rolls, saves, and skill checks, while each of your foes takes a –1 penalty on such rolls."
A spell is not a weapon, so it doesnt apply to spell damage. Divine Power and Divine Favor also specificy weapon damage rolls. I cant think of one off hand that would apply to a spell.