The UESP informs me that Wuuthrad deals 1.2x damage to Elves, or an extra 20% of damage (which is equivalent to taking a point in the Barbarian perk). But is that extra damage based on the base damage of the weapon, or on the damage you do when you've got a high 2-handed skill and damage-increasing perks?

Wuuthrad's base damage, according to UESP, is 25. 1.2 x 25 = 30, which means Wuuthrad's effect translates into 5 extra points of damage if the extra damage is keyed off that base of 25.

But suppose you have enough skill and perks so that Wuuthrad deals 100 damage (I don't think this is possible, but it's an easy number for me to do math with ). Would the Elf-specific damage then become 1.2 x 100 = 120, for an extra 20 points of damage? Or would it remain, always and forever, 5 points of extra damage against Elves?

Getting a weapon to 100 from 25 should be possible, especially if you temper it and have lots of points and perks in the specific skill and have clothing or potions boosting that skill. Right now I have a one handed Dragonbone sword that does 524 damage (plus 14 burn damage) if I'm wearing the right equipment, and I know I can do better than that if I remake some of my stuff.

As for your actual question, I'm guessing the bonus does apply to all of the above, not just the base damage, but that's just a guess.

I would assume that it's +20% of whatever *your* damage is with the weapon, as otherwise they could have just written "does an extra 5 points of damage against elves" or whatnot. I could be wrong, of course.