I've just started a house rule combining the 3.0 and the 3.5 rules for magic bows and arrows. In 3.0, the to hit and damage stacked, but not for purposes of damage reduction. Only the projectile counted for damage reduction. (+1 arrow and +2 bow were +3 to hit and damage, but only +1 to overcome damage reduction.)
In 3.5, they don't stack at all, but the projectile counts as the highest plus for damage reduction. (as above, +1 arrow and +2 bow would be +2 to hit, damage, and to overcome damage reduction.)
I'm going in between. Bonuses from both weapon and projectile stack for to hit and damage, but only the highest bonus counts for damage reduction. That way, normal arrows from a +1 bow would count as +1 for damage reduction. And using the example above, +1 arrow and +2 bow would be +3 to hit and damage, and +2 for damage reduction.