Hunter shot damage is based on your a percentage of your weapon damage + a percentage of your Ranged Attack Power + a base amount. For example: Killshot's damage is 150% of your weapon's damage + 30% of your RAP + 325. Basically to hit harder you want higher damage weapons which means slow weapons. Stay away from weapons faster than 2.5 because they aren't meant for hunters. Even if the DPS is higher go with the one with the higher damage.
Weapon Damage and AP aren't the only stats you need though. Hit, crit, haste and Mastery rating are all important too. You get 2 Attack Power and 1 crit rating from each point in Agility.
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“It is better to be rich and healthy than poor and sick” - Dave Barry
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