As far as I understand, there's no 100% software based crossover. Reason being that controlling separate audio outputs from the same source normally would require specific hardware (i.e. multiple audio cards) -- to allow for playback of different (filtered) streams of sound at the same time. While some sound cards have some hacked drivers to simulate multiple cards on its different outputs, I'd say your best bet is still to go with hardware (passive crossovers are very easy to install and very cheap too).
It is however, VERY easy to add a 100+ Band EQ for the whole setup (for all speakers though).