Bracers of Armor vs. Incoporeal Touch Attacks
Ruling by the sage in this months dragon Magazine Sage has said even though it's not listed in the item description Bracers of Armor work the same way as the Mage Armor spell needed to create them.
From the SRD
Since mage armor is made of force, incorporeal creatures can’t bypass it the way they do normal armor
So touch attacks ignore them but incorporeal touch attacks must deal with them.
Briliant Energy vs. Armor of Fortification
From the SRD
A brilliant energy weapon has its significant portion transformed into light, although this does not modify the item’s weight. It gives off light as a torch (20-foot radius). A brilliant energy weapon ignores nonliving matter. Armor and enhancement AC bonuses do not count against it. (Dexterity, deflection, dodge, natural armor, and other such bonuses still apply.)
And again From the SRD
Fortification
When a critical hit or sneak attack is scored on the wearer, there is a chance that the critical hit or sneak attack is negated and damage is instead rolled normally:
Regardless of logic the only benefit Briliant Energy provides is to bypass armor and enhancement AC bonus'. All other benefits of the armor are applied. For example if you Crit someone with a Shield of Fortification I assume you didn't go THROUGH the shield to hit them, you just found a better spot but the fortification effect is still active for that person as well.
By the way Bracers of armor are still an armor enhancement so briliant energy weapons do bypass them since they are not incorporeal. There is Ghost Touch weapons for that.