In short, P=qV is the general formula for finding electrical potential energy and P=(1/2)QV is a special case of that formula for capacitors.
If that doesn't satisfy you, I'll go on to more detail below which will hopefully help.
PE=qV
This comes from the definition of voltage which is energy contained per coulomb of charge so:
V=energy/q
Thinking of this energy as potential energy and rearranging the equation we end up with what you mentioned(P=qV). As for uses of this equation, one classic example can be found here:
http://answers.yahoo.com/question/index?qid=20090121192721AAftcJg
In this, V=Ed is used first to find V, then P=qV is used. V=Ed is another handy formula, just remember that the d refers to the distance traveled parallel to the electric field and perpendicular distance does not count because energy increases or decreases only in the direction of the force (think of W=Fd) so you may need to use some trigonometry in some problems to get the proper distance.
U=(1/2)QV
This is the above formula applied to capacitors. Since capacitors go from 0 Volts to some maximum voltage as they charge, we use (1/2)QV to take an average of the energy involved. You should also recognize that the formula for capacitance, C=Q/V can be used to make different forms of (1/2)QV through substitution so:
Energy stored in a capacitor(U)=1/2 QV = 1/2 CV^2 = (1/2 Q^2)/C
One other thing to know involving this formula is its relation to C=kA/d where C is capacitance, k is the dielectric constant, A is area of the capacitor plate, and d is distance between the plates. It's good to use these 2 formulas to better understand what happens when changing aspects of a capacitor. For instance, you can see that increasing the distance between plates would lower capacitance, but increase energy stored(U). (Always use U= (1/2 Q^2)/C during this type of logic check because V is constantly changing as the capacitor charges so U=1/2CV^2 is useless for this because you want all other variables besides C constant. Q is constant which is why the other form is used.