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:
Favored Enemy (Ex) At 1st level, a ranger may select a type of creature from among those given on Table: Ranger Favored Enemies. The ranger gains a +2 bonus on Bluff, Listen, Sense Motive, Spot, and Survival checks when using these skills against creatures of this type. Likewise, he gets a +2 bonus on weapon damage rolls against such creatures.