HOMER can model variable-speed generators.  The principal feature of a variable-speed generator that distinguishes it from a fixed-speed generator is its fuel consumption curve.  On the Fuel tab of the Generator Inputs window, you enter the generator’s fuel curve, which specifies its fuel consumption versus its power output.  HOMER assumes that fuel curve is a straight line, for which you enter the slope and intercept.  But the Fuel Curve Calculator window lets you simply enter the points on the fuel curve, and it does the calculation to fit a straight line to the curve and calculate the slope and intercept coefficient.

A variable-speed generator will tend to have a fuel curve with a lower intercept and a higher slope compared to a fixed-speed generator.  For example, the graph below compares the variable-speed VG-50 by CVT Corp with two fixed-speed generators of similar size.  (Source:  http://www.cvtcorp.com/docs/MKT-1000-D%20_White%20Paper_.pdf)  You could enter any one of these fuel curves into HOMER’s Fuel Curve Calculator window.  The assumption of linearity may be slightly less accurate for a variable-speed generator, but at least for the example below, it is sufficiently accurate in my opinion.