I go to an independent tire and service dealer for most things. For example, a transmission service at the dealership is $199 with the Honda fluids and $99 at my new service center. The rear diff service was the same $99 for both dealers, though. The dealership rips you off on labor charges. I would only go to the dealership for valve adjustments (they have more experience), PCM updates, or anything that can't be done locally.
As for brakes, they're generally expensive services, but for my wife's 2012 CR-V, I paid $159.23 for new rear pads, turned rear rotors, and clean and lube caliper job.