Clarity..
Where I got:
Capable of independant choice. If you limit it to capable of physical action, then one who is paralyzed can be considered not a creature. By stating it as capable of independant choice you avoid this trap. A soul has the independant choice of returning when a raise dead spell is cast, but cannot do anything else. Unless you count traveling to the Outer Planes
Is the soul the dead creature? ... The dead creature is split into dual existance, one part is the Corpse and the other the soul. Split along the physical/meat and spiritual/mind. The soul can be pulled back into the Corpse via certain spells and can be contact by certain spells, but otherwise has no impact on the world. The soul holds all the character features, memories, and spiritual existance. The Dead Creature is an empty husk.
Specific expections to this are the creatures who do not have a dual nature or were never alive to begin with. Those creatures, specifically Constructs, Outsiders, and Elementals, do not have souls released upon thier death.
Rereading the 'Dead' condition, "Dead: The character’s hit points are reduced to –10, his Constitution drops to 0, or he is killed outright by a spell or effect." .. I was in error. There is no CON adjustment, or any other stat adjustment when you are dead. The sentence refers to how you gain the condition.
I also reread the raise, ressurect, and reincarnate spells. The wording of those spells bring me to revise my POV.
Instead of having 2 types of Corpses, there is only one.
The Corpse is an empty husk, a close relative to an inanimate object. Useful mainly as a material focus for the raise spells. It maintains the physical aspects, like wings, claws, and racial stat modifiers. It gains a hardness and hitpoints based on its material make-up as an object and possibly retains all or part of racial resistances to elements. Touching the Corpse provides a spiritual link to the Dead Creature, allowing the casting of the various Raise spells.
The Dead Character is the soul, which carries the; class, stats, SR, etc...
This is 'proven' by reading the Reincarnate spell. With that spell a soul is brought back into a new body. The new body modifies the characters physical stats but you dont re-roll them. If you were a weakling Elf and reincarnated as a Bug Bear, you will still be a weakling.
RigaMortis...
Animals are not listed as not having souls, so by RAW, they have them. As do Plants.
Intelligent Weapons do not have souls, by RAW. ALtho it would be an interesting house rule. I had a cmapaign once where Intelligent items were made by forcing a soul into them, which led to some interesting moral issues.
Greater Scry would have to be a judgement call by the DM.