So, how does one deal with enemies who have Fortification? Are there feats to reduce it, or a prestige class that specializes in it? Or do you just send in the fighter and let him beat down the enemy?
You deal with enemies with fortification the same way you deal with any enemy immune to critical hits: energy damage, persistent normal attacks, grapple+pin+rope, save or dies, mental control, walls, sundering their armor or shield, shatter....
there's lot of options at your disposal. Critical hits and sneak attack are nice, but hardly leave you toothless in the face of the enemy.
The last.
If you are high enough a level, Disjunction always works when faced with those pesky magic items other players rely on.
MA
Barbarians get a rage power that blocks enchantments on things they sunder temporarily. That would stop it.
Or they could just smash it. That would also stop it.