Impossible in the Flash client current state. ALL sound is binary, it's either on or off. There is no way developers can control the actual volume.
However before I departured I did figure out a method that would allow specific sounds to be muted.
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Well, you could always have the volume controls for the Flash client to be "knob" style like very low, low, medium, high, very high, and instead of dynamically adjusting the volume of a single sound file, just create 5 different files at these volumes - it's obviously pretty ghetto and would work awkwardly in some ways, but it'd be better than nothing.
That requires editing a lot of sound files though... I had only wanted it for PM notifications, but now even those have changed to be more advanced, so it wouldn't be an easy task overall.