I wondered about this all the way through Borderlands and now I'm seeing the same thing in Borderlands 2. If a weapon has, for instance, 200 damage, and a modifier that says "+20% weapon damage", does that mean that the weapon actually has 240 damage or that the weapon had 166 damage before the mod was applied?
The answer to this question sort of answers the question for Borderlands, but I'm still not sure in Borderlands 2.
Best Answer
Skill bonuses, badass bonuses, and bonuses from other equipment are applied after the item card. Whatever modifiers are listed on the item card are applied before item card totals.
Everything you see on the weapon card is final (for the weapon). If the card says 200 damage, the gun will do 200 damage on a body shot in the hands of an unskilled, dull, non-badass character. In your example, the gun did 166 damange before a modifier.
More often bonuses listed on the item card have no corresponting totals displayed, so they are important - like critical damage or stability.