D&D 3.5 Rules FAQ

Can rangers be denied their favored enemy bonuses? For example, if a fighter is wearing armor of fortification, which has a 25% of negating sneak and critical damage, successfully blocks the critical, will the ranger's +2 damage bonus also be negated?

Evil Genius writes:

In 3.0, the answer was "yes". The ranger's favored enemy bonus specifically stated that while the bonus to Bluff, Spot, Listen and Track (now Survival) never went away, the damage bonus only affected creatures subject to critical hits. Therefore, if you chose undead or constructs or oozes as your favored enemy, you would not get the +2 to damage. It would follow that if your Fortification triggered that you would not take the additional +2 damage from a Favored Enemy bonus. Read the "Favored Enemy" entry on the d20 SRD.

Forward to 3.5, the answer is now "no". In the ranger class description, it no longer says that the +2 bonus is contingent on the favored enemy being subject to critical hits. So now there shouldn't be any way to negate the +2 Favored Enemy bonus.

NukeHavoc writes:

The one exception to this is polymorph. A ranger’s favored enemy bonus is based on knowing what the foe is, so if a creature that is a ranger’s favored enemy polymorphs into another form, the ranger is denied his bonus. Read the "Polymorph" section of the the Natural and Special Abilities section of the d20 SRD.