Usually the rescue organisation's fees include the cost of spaying or neutering, vaccinations, microchip, and perhaps more. For example, here's what the adoption costs for the ASPCA adoption centre in Manhattan include:
The ASPCA Adoption Center offers you and your new animal companion the
A leash and collar or cardboard pet carrier to help you bring your new
companion animal home.
Spay/neuter surgery, up-to-date vaccinations, registered microchip,
heartworm testing, FeLV/FIV testing for cats and an
overview of your pet's medical care.
A certificate for free follow-up veterinary care and medical support at
the ASPCA Animal Hospital (valid for 14 days after adoption).
Literature and information about animal behavior and what to expect
from your new pet.
A collar with personalized identification tag.
Sometimes the cost will include pet insurance for a few weeks or months. And if you want to use your own vet for spaying, neutering, or vaccinations, some shelters might rebate that part of the cost when you present a receipt from your vet. Check around.
So if you are adopting a kitten or puppy, be sure to factor in the cost of spaying or neutering, vaccinations, microchipping, etc. before you compare prices.
Another thing to consider: In my experience, rescue organisations are very good at matching you with the pet that's best for you (in terms of temperament, behaviour, activity level, etc.). They have a variety of animals, and they have an incentive to make sure that you're happy with the pet that you get.
Also, consider that part of the adoption cost that you pay a shelter helps to keep that shelter running.