So I've done some searches on this and I am still not positive about the answer yet.
What armor bonuses (if any) are in effect when a driud is wildshaped?
Regular Armor bonus (plus any enhancement bonus) doesn't apply.
Natural armor bonus (from amulet or barkskin)... does it stack with bonus from wildshape?
Deflection armor bonus... I assume this applies.
Shield bonus (from a shield)... does it apply?
Any others I missed...?-dm
Different AC bonusses:
Armor bonusses - Generelly no, but the following can be done: Armor with wild ability, barding (assuming someone puts it on you after changing form (and you got one for the form, and last possibly armor like bracers of armor (It is a GMs call, this one, there is a lengthy discussion whether it continues to function or not).
Natural armor bonus - Amulet and barksin stacks with your existing natural armor, because it is an enhancement bonus.
Deflection bonus - works
Shield bonus - No, in my opinion (although there is a discussion of this based on the exact wording of the polymorph section). But you can make a wild shield for a shield bonus.
Dodge bonus - functions without a problem.
Others (such as luck or insight) - works as normally.
So I've done some searches on this and I am still not positive about the answer yet.
What armor bonuses (if any) are in effect when a driud is wildshaped?
Regular Armor bonus (plus any enhancement bonus) doesn't apply.
Natural armor bonus (from amulet or barkskin)... does it stack with bonus from wildshape?
Deflection armor bonus... I assume this applies.
Shield bonus (from a shield)... does it apply?
Any others I missed...?-dm
ONE "Enhancement Bonus to Natural Armor" (barkskin OR amulet) does stack with your ONE "Natural Armor Bonus" to determine your total Natural Armor Bonus. Then that total natural armor bonus does stack with any armor bonus you might get from something like horse barding, or wild armor enhancement.
If you have more than one source of enhancement bonuses to natural armor, you pick the highest one, and you must choose the base natural armor bonus for the form you're currently in.
So for example,
Lets say I'm a Sauhagin druid. Sauhagin have a 5 natural armor bonus. A sauhagin wearing studded leather armor and no dex or other modifiers would have an 18 AC. 10+5natural+3armor.
If this druid wildshapes into a medium animal, he loses his natural armor bonus from his native form, loses his armor bonus from his leather armor, and adopts the natural armor bonus of his new form, which is +2. In this particular case, his AC goes WAY down because he loses his 5 natural armor and replaces that with the 2 natural armor of his new form. His AC would be 10+2natural=12.
Now lets make it complicated. That same druid of let's say 6th level wears a amulet of natural armor +2, and also casts barkskin. The amulet gives him an enhancement bonus to natural armor of +2, but the barkskin spell gives him an enhancement bonus to natural armor of +3. He takes the higher of these two as an enhancement bonus to natural armor.
So in his native form, his "natural armor bonus" is 5+3=8, and his total AC is 10+3+8=21. If the barkskin expires, his AC drops to 20. If he wildshapes before it expires, his "natural armor bonus" is 2(beastshape)+3(enhancement)=5, and his AC is 10+5(natural)=15.
Confused yet? Wait til you're higher levels and you pretty much have to figure this crap out in advance and write it all down before you start playing, otherwise you'll never figure anything out. CMD is a real hoot to calculate.
About shield bonus and wildshape.
This part of the rules has been errata'd and now it's pretty clear that they don't transfer.(unless of course you have a wild shield)