Nearly all skills in Diablo 3 are based on a weapon damage value. This measurement can be confusing because weapon damage can be misinterpreted to be the damage listed on your individual weapon tooltip itself, rather than your actual final "Character damage " after modifiers (such as +attack).

When Skills refer to doing "X% weapon damage", it is referring to your final adjusted damage "Character Damage" after passives and all stats/items, not the damage listed on the weapon itself. This final adjusted Character damage includes the total +Attack modifier (from the Attack Attribute) and any other item stats that affect your damage. It is simply your final damage as if you are attacking with a base attack. This does in fact mean that slower weapons will do more damage than faster weapons for that swing or cast, but it will take longer to perform the cast or swing. While this may appear to favor slow weapons, it is offset by both the ability to attack faster therefore more often, as well as faster resource generation via generator skills. Skills with cooldowns may favor slower weapons depending on your play-style, as you cannot perform that skill more than once, however the faster resource generation of faster weapons is used to offset this advantage by giving you extra resources hence doing more damage.