http://en.wikipedia.org/wiki/Square_wave
This is a job for Fourier analysis. Simply take the square wave, analyze it as a sum of sine functions, and then do a separate analysis of the circuit for each sine function.
For example, you have a square wave voltage applied to a load which consists of an ideal filter and then a resistor. This imaginary load essentially has infinite impedance for all voltage components other than fundamental, and is a resistor for the fundamental voltage component.
You use Fourier analysis to figure out the voltage of the fundamental component, and then just use Ohm's law to figure out the power delivered through the circuit by the fundamental component.
If you take a +-1V 50% square wave and feed it through an _ideal_ filter that will only pass fundamental, then you will end up with a +-4/pi sine function. Read that again
The peak voltage of the fundamental component of the a square wave is greater than the peak voltage of the source square wave. Its right there in the Fourier series, and has real application in VFD design.
VFD aside: the way that the VFD works, the output is synthesized by using IGBT devices to switch an internal DC supply to the output. The peak voltage of the output waveform is set by the internal DC voltage (usually, when a half bridge topology is used, output peak to peak voltage is equal to the DC voltage). A very common trick is to _intentionally_ add a bit of third harmonic to the output. This lets the fundamental peak to peak voltage exceed the DC rail voltage. The composite waveform output is limited to the DC rail voltage, but the fundamental component can be slightly greater. A three phase motor will not pass third harmonic, and thus acts like a near perfect blocking filter for this component. The net result is that the motor windings 'see' a voltage that is greater than the inverter can supply.
-Jon