all weapons have a different base damage. the reason your chakram has higher damage than flintlock or bow is that it starts with 300% primary damage. it does a lot of damage, but until it gets back into your hands, you are weaponless. flintlocks fire very fast with long range, and bow fires arrows that home in on the enemy. dagger is only short range, but very fast and helps you use your special attack sooner. all class weapons are like that.
class weapon skills improve which ever weapon you are using, and then there are affixes for more buffs and bonus's.
DPS isn't the actual damage your weapons does. that is just the potential damage it can do in one second. it is affected by skills, talents, affixes, and item level.
some buffs increase your damage, but because of the way the work, don't show up in the DPS, like Bloodmagic, which gives a damage bonus based on how much HP you have, which changes a lot during a battle.