Innate Weapon Damage
Torchlight 1.14: Has the 20% effect you'd expect, but note that multiple damage types DO stack, so if you have a weapon with 100 Fire damage and 100 Poison damage, Ember Bolt gets 40 damage added to it, not 20. This is not how most people thought it worked. When dual wielding, only the highest damage appears to be used (this is per-hit damage, not DPS). They do not appear to be averaged, added, or alternated; the damage is consistent.
Torchlight 1.14: No effect; the 20% bonus appears to be based on effect damage, not on the listed DPS.
Damage Bonus Gem On Weapon OR Armor
Torchlight 1.14: Has complete, 100% effect. If you add a +100 Fire Damage mod to your weapon, Ember Bolt does 100 more damage. If you add a +100 Poison gem to your boots, that adds another 100 to Ember Bolt. This is almost certainly a BUG. Sure explains why Ember Bolt got so popular after Ember Lance was tuned down.
Percent Damage Bonus On Weapon OR Armor
Torchlight 1.14: Has complete, 100% effect if the element matches. "Magical" does nothing, but "ALL" (see text notes above) has 100% effect.
Knock Back Bonus On Weapon OR Armor
Torchlight 1.14: Enemy is knocked back.