Diablo – Why does Disintegrate deal more damage than Ray of Frost

To answer the question posed in the initial question: Only if you had 0 intelligence and no other damage bonuses!

Base damage is simply weapon damage + any damage bonus from gear (+elemental damage is effectively "+damage" as far as the system is concerned).

The formula is roughly as follows

Base Damage =
        (weapon damage range + bonus damage from gear)
        × bonus from primary attribute^†
        × other class bonuses from skills.

Ability Damage =
        Base Damage (as above)
        × % Weapon Damage listed on the ability.

^†1 primary attribute = +1% bonus damage

Weapon speed doesn't come into play at all when calculating damage from abilities.

What this means is that weapon speed is balanced as a stat; either you deal more damage per hit (by picking a slower weapon), or you use more abilities (since weapon speed affects animation time). DPS is entirely useless as a comparison metric unless you're only auto-attacking.

Bonus elemental damage is overridden when using a skill that does damage of a particular specified element. You still receive the damage bonus, but it is no longer of the element specified by the item.

For example, if you have a weapon that does 20-40 damage, and a bonus of +4-8 Fire Damage, and use an ability that does 100% Weapon Damage as Lightning Damage, you would do 24-48 lightning damage with that ability.

If the ability does not specify a particular damage type, then it will deal damage based on your weapons inherent damage type.