@Brad Larsen is correct, in that the professionals (licensed) PM will not be able to discuss service costs due to price-fixing concerns.
Much of the decision to charge for specific items, or as a PM, to either charge for the services or to include them in a set management fee, depends on your perspective of risk and time management.
As an individual property owner and landlord, my concern (one risk) would be about driving away your renter with fees, when a renter at an apartment or someone renting through a PM would probably only pay an application fee.
As far as pet fees /deposits go, it can also be several ways. A one-time non-refundable fee, an increase in rent for the animal, or an additional deposit that is refundable if there is no damage.
The question is, can you manage it, can you be consistent, and can you estimate with any comfort which is best for you. And be sure to disclose any fees you expect to charge UP FRONT during the application.