Suppose I'm playing a ranged character. I am standing with an ally between me and my enemies, which grants "+2 defenses" for cover. I decide to further go prone. Do I now have a "+4 defenses", 2 from cover and 2 from prone? Or is "going prone" a 'cover bonus' and therefore nonstacking with the cover bonus from my ally?
Prone gives you:
You get a +2 bonus to all defenses against ranged attacks from nonadjacent enemies.
Cover gives the attacker
-2 Penalty to Attack Rolls (for ranged attacks)
So against non-adjacent ranged attacks you have a +2 bonus to all defenses and the attacker takes -2 to his Attack.
Effectively your defenses are 4 higher.
Cover does not grant you a +2 bonus to defenses: it imposes a -2 (unnamed) penalty to attacker's attack rolls.
Being prone grants you a +2 (unnamed) bonus to defenses against ranged attacks from non-adjacent enemies.
So, against a ranged attack from a non-adjacent enemy you got a +2 to all defenses for taking cover behind your ally and the attacker gets a -2 to hit you because you are prone.
As a reminder, however, unnamed bonuses stack unless they're from the same named game element.