You must remember that with a capacitor the value
of the voltage quoted in the formula is the FINAL voltage when fully charged. During the
charging process the voltage builds up from zero.
You know the formula C = Q/V so you
can see that as the charge on the plates (Q) increases so does the voltage between
them.
Think about a graph of Q against V (because Q = CV and C (the capacitance of a
given capacitor) is constant) it will be a straight line.
Since energy (as you say) = VIt =
QV the area below this line (charge x voltage) is the energy stored and this is ½
QV.
Using C = QV gives the other versions of the formula ( ½ CV2 and ½
Q2/C).