Damage enchantments are nice, since they add to the minimum damage done (level 9 enchantments can add 24 to your normal or magical damage). However, it isn't really that big of a difference. There are cases where adding an enchantment could make one particular weapon better than another, but later in the game an enchantment slot on weapons is fairly common. There are some special weapons that can have 2 or rarely 3 enchantment slots. Late in the game damage bonuses start showing up on weapons, as well (listed in the blue bonus section), which can exceed what you would get with an enchantment.
Enchantments need to be taken into account if you want to calculate the DPS, but it isn't a large enough effect that you should take it into account more than which playstyle you prefer.
