| My guess is that all the pieces are there. You just need to figure out a way to connect them.
LADSPA is a sound processing library and plugin framework that can do lots of things with a sound wave.
Jack can connect in/outs and can also work with then at real time. Is the preferred framework for low latency.
I don't know how to do what you want, but whatever the solution is, it will surely involve these two pieces. I also think that, once kde4 is out and phonon is fully working, this kind of stuff might get much simpler to implement (that will not help now, though).
EDIT: Now that i remember, mplayer supports both jack and ladspa. It also supports piping to/from files so I guess that there might be a way to implement an mplayer based solution for this problem. I don't know how, but maybe it's possible. | 
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