There is a LADSPA plugin to convert Stereo to M/S. Then you just run different EQ settings on each of the outputs before later combining them (this is trivial to setup in Non Mixer). However, watch out for using EQs with different internal latencies. Also, I would expect to end up with phase isues if not using a linear-phase EQ (the only one of which I am aware is the one in Jamin). But from what you're aiming to do in the first place, I imagine you don't really care that much about correctness.