Does a player that becomes an outsider as part of a class feature still count as being humanoid for the purposes of things like favored enemy?
Favored Enemy specifically tracks types and subtypes of creatures; becoming an Outsider supplants your normal type, changing the Favored Enemy types you count under. In the flavor, Outsiders are composed of a different essence than other Material beings, making their essence and anatomy subtly different. In RAW, it's a simple type change, with all the things that entails.
For more on Favored Enemy, check the SRD link here, but the important part is here: