I want to do a PV run in Homer.  At the input screen for PV capacity, it isn't totally evident to me if the input should be gross DC capacity of the array or net AC output capacity after accounting for I^2R losses in the wiring, inverter losses, dirt buildup losses, and degradation over time.  From the help system, theformula for output that is reduced by the degradation factor appears to indicate that the input is DC capacity. 

You should enter the gross DC capacity.  The derating factor is meant to account for I^2R losses, soiling losses, and the reduced efficiency of the panel at high temperature.  The panel's rated capacity should already account for the degradation over time (a panel rated at 40W should initially put out a bit more than 40W under standard test conditions) but if not you should include that in the derating factor too. But don't include inverter losses in the derating factor.  HOMER models the inverter separately and it has its own efficiency.