the SRD says this about stacking:
In most cases, modifiers to a given check or roll stack (combine for a cumulative effect) if they come from different sources and have different types (or no type at all), but do not stack if they have the same type or come from the same source (such as the same spell cast twice in succession). If the modifiers to a particular roll do not stack, only the best bonus and worst penalty applies. Dodge bonuses and circumstance bonuses however, do stack with one another unless otherwise specified.
Does the same attribute modifier necessarily count as the same source?
Case A: for example, would the Wisdom modifier melee bonus damage from the epic prestige class Perfected One (Epic Level Handbook) stack with the Wisdom modifier bonus damage of the Shiba Protector prestige class (Oriental Adventures)?
Case B: would the bonus type make a difference? As an abstract example, would adding the Charisma modifier as a sacred bonus to reflex saving throws from class feature A and a the Charisma modifier as an insight bonus to reflex saving throws from class feature B stack?
Case C: would the kind of enabler matter? For example, if we had the Gauntlets of Heartfelt Blows (adds the Charisma modifier as bonus fire damage to melee attacks) and an imaginary class feature that adds the Charisma modifier to damage - would they stack?