Two of the domains listed in D&Dg (Creation and Artifice) specifically say that the bonuses (+1 and +2) to Conjuration (creation) spells become +3 if the cleric has both domains. I take that to mean that all such bonuses stack.
I have seen other instances where domain caster levels stack, but I can't think of them right now.
I have seen other instances where domain caster levels stack, but I can't think of them right now.