Well, it's actually t's pretty much the same as in English:

Does it hurt (you)?

Where does it hurt (you)?

etc. ...

the "es" refers to the injury (as it does in English).

"Was tut es dir weh?" is the only one of your examples which doesn't make sense -

you would ask "Was tut dir weh?" -

The answer could be, for instance: "Der Kopf", "Der Fuß", etc.

(same meaning as "wo tut es (dir) weh?")

Was fragt man:
Wo tut es dir weh? - ok
Wo tut es weh? - ok
Worauf bezieht sich dieses es? see woody's answer
Was tut es dir weh? - no, that's wrong
Was tut dir weh? - ok
Was tut weh? - ok

Vielen Dank!

Nachtrag zu woodys #3:
Auch noch: "Was tut dir weh?" - "Deine Missachtung!"