Damage bonuses apply to each instance of damage. If a card or power breaks out damage in any way, each instance is increased appropriately.
Example 1: Fanatic’s “Exorcism” power normally does 1 melee and 1 radiant damage. If something is increasing damage by 1, it will do 2 melee and 2 radiant damage.
Example 2: When used, Haka’s “Savage Mana” power does 2 toxic damage for each card beneath it being destroyed. If something is increasing damage by 1, it will do 3 toxic damage for each card beneath it being destroyed.
Example 3: Tachyon’s “Lightspeed Barrage” does not work in the same way as the first two examples. The card reads, “Tachyon deals 1 target X melee damage, where X = the number of Burst cards in your Trash.” In this instance, if she has 9 Burst cards in her trash and there is a +1 to damage, she will deal the target 10 damage instead.
Example 4: Bunker’s “Omni-Cannon” is similar to example 3. The card’s power portion reads, “Destroy all cards beneath this card. Bunker deals 1 target X energy damage, where X = 2 times the number of cards destroyed.” If there were 5 cards under it, and a +1 increase to damage, the power would deal the target 11 damage.
Example 5: Tempest’s “Vicious Cyclone” is another example where this does take effect. The card reads, “Play this card next to a target and Tempest deals that target 2 projectile damage. At the start of your turn, you may discard up to 3 cards. Tempest deals this card’s target 1 projectile damage for each card discarded this way. If the target leaves play, destroy this card.” Normally, if you discard 3 cards, you will deal that target 3 damage (1 + 1 + 1). However, if there is a +1 to damage, discarding 3 cards would deal the target 6 damage ((1 + 1) + (1 + 1) + (1 + 1) = 6).