Are all bonuses to AC treated as separate? If a character is wearing a +5 padded shirt of heavy fortification and someone casts mage armor on him, does he keep the +1 enhancement bonus and fortification?
The +5 heavy fortification padded armor adds a +6 armor bonus to AC, and the heavy fortification effect.
Mage armor adds a +4 armor bonus to AC.
Since these are both armor bonuses, they overlap rather than stack, so you pick the higher. Thus, the mage armor is effectively doing nothing (except when attacked by incorporeal foes, since they ignore physical armor but not mage armor).
If you had a +1 heavy fortification padded shirt (+2 armor bonus to AC instead of +6), then the mage armor bonus would “win” and you would have a +4 armor bonus to AC. You would still have the heavy fortification effect.
The general rule for stacking is that when two bonuses are named the same way they don't stack and you pick the better one, and when they are named differently they do stack and you can add them together.
Both the armor and the mage armor spell give a "+n armor bonus to AC". Because both are referred to as "armor" bonus, they don't stack. If one of them would be called differently, like "+n robustness bonus to AC" or something, they would stack.
The other answers are correct, however there are a few specific exceptions to be aware of:
Armored kilt lets you add itself to another set of armour: http://www.d20pfsrd.com/equipment---final/armor http://www.d20pfsrd.com/equipment---final/armor/armored-kilt
Different types of AC (for example shield (whether equipment or spell), natural armour, dodge bonus and real armour) all stack. This can get subtle as well, for example:
- If you had Chainmail +6 AC.
- Cast Mage Armour - no effect still +6 as you have a +4 and +6 both of the same type.
- Added an Armoured kilt - you now count as heavy armour and +7 AC
- Put on an Amulet of Natural Armour +4. That stacks, you now have +7AC for armour and +4 for natural armour for total of +11.
- Cast Barkskin this provides an enhancement bonus to your natural armour of +2. But so did the Amulet of Natural armour which is already giving more so you remain on +11. As with the armour bonusses you now have two separate sources of enhancement to natural armour so only the strongest applies.
- Now get put all of that onto a Lizardfolk, which has a +2 natural armour bonus. This is natural armour not an enhancement to natural armour so it does stack. This puts the Lizardfolk to +13
So just be really careful to look at "what is the type of the bonus" and "what is the bonus targeting". You can have "armour", "dodge", "natural armour", "enhancement to natural armour", etc and they will all combine but you can only have one of each.